diff --git a/.changeset/route-input-usage-prefill-fixes.md b/.changeset/route-input-usage-prefill-fixes.md
new file mode 100644
index 000000000..7c4cacb26
--- /dev/null
+++ b/.changeset/route-input-usage-prefill-fixes.md
@@ -0,0 +1,12 @@
+---
+"agent-bundle": patch
+---
+
+Route catalog and MCP prefill correctness fixes from post-merge review: CLI
+usage summaries mark repeatable named options with the same ` ...` operand
+suffix the generated help prints; optional booleans without a schema default
+keep an unset state (a three-state omitted/true/false control) instead of
+submitting an explicit `false` the handler can observe; and a stale
+Routes-page prefill naming a tool the server no longer advertises surfaces a
+missing-tool notice instead of silently attaching the prepared arguments to
+the first advertised tool.
diff --git a/packages/workbench/src/mcp/mcp-page.css b/packages/workbench/src/mcp/mcp-page.css
index 81370cafc..e8c1b4f0f 100644
--- a/packages/workbench/src/mcp/mcp-page.css
+++ b/packages/workbench/src/mcp/mcp-page.css
@@ -337,6 +337,14 @@
   color: #a8b8ca;
 }
 
+.mcp-page-missing-tool {
+  background: #3a1f24;
+  border-left: 3px solid #f28b82;
+  color: #ffd9d4;
+  margin: 0 0 0.75rem;
+  padding: 0.55rem 0.75rem;
+}
+
 @media (max-width: 42rem) {
   .mcp-page-heading,
   .mcp-page-catalog li,
diff --git a/packages/workbench/src/mcp/mcp-page.tsx b/packages/workbench/src/mcp/mcp-page.tsx
index 1dda422dd..fa4fa6c4e 100644
--- a/packages/workbench/src/mcp/mcp-page.tsx
+++ b/packages/workbench/src/mcp/mcp-page.tsx
@@ -1240,7 +1240,13 @@ export const McpPage = (props: McpPageProps) => {
   const prompts = catalogItems(model.catalogs.prompts, 'Prompt');
   const resources = catalogItems(model.catalogs.resources, 'Resource');
   const resourceTemplates = catalogItems(model.catalogs.resourceTemplates, 'Resource template');
-  const selectedTool = tools.find((item) => item.name === toolName) ?? tools[0];
+  const matchedTool = tools.find((item) => item.name === toolName);
+  const selectedTool = matchedTool ?? (initialToolPrefill === undefined && toolName === '' ? tools[0] : undefined);
+  const missingToolName = initialToolPrefill !== undefined
+    && model.phase === 'ready'
+    && !tools.some((item) => item.name === initialToolPrefill.toolName)
+    ? initialToolPrefill.toolName
+    : undefined;
   const selectedPrompt = prompts.find((item) => item.name === promptName) ?? prompts[0];
   const active = Object.values(model.activeRequests);
   const controls = mcpPageSessionControls(model.phase, pendingActions, onResetSession !== undefined, serverCatalogState);
@@ -1428,6 +1434,9 @@ export const McpPage = (props: McpPageProps) => {
         <strong>Tool call prefilled from Routes</strong>
         <p>{initialToolPrefill.serverName} · {initialToolPrefill.toolName}</p>
         <pre><code>{display(initialToolPrefill.arguments)}</code></pre>
+        {missingToolName === undefined ? undefined : <p className="mcp-page-missing-tool">
+          The server no longer advertises the &quot;{missingToolName}&quot; tool. The prepared arguments were not applied to another tool.
+        </p>}
         <p>Open the session and use the existing call control when you are ready. Nothing runs automatically.</p>
       </aside>}
       <div className="mcp-page-catalog-grid">
diff --git a/packages/workbench/src/routes/routes-model.ts b/packages/workbench/src/routes/routes-model.ts
index f923611f6..df48a9fd1 100644
--- a/packages/workbench/src/routes/routes-model.ts
+++ b/packages/workbench/src/routes/routes-model.ts
@@ -213,24 +213,35 @@ export const routeCatalogHasKind = (catalog: RouteCatalog, kind: RouteManifestKi
 export const routeCatalogServerCount = (catalog: RouteCatalog): number =>
   catalog.servers.length;
 
-const defaultDraftValue = (schema: RouteInputPropertySchema): RouteInputDraftValue => {
+/**
+ * An optional boolean without a schema default stays out of the draft: a
+ * `false` initialization would submit `{ key: false }` where the author's
+ * handler observes an omitted property, defeating optional semantics.
+ */
+const defaultDraftValue = (
+  schema: RouteInputPropertySchema,
+  required: boolean,
+): RouteInputDraftValue | undefined => {
   if (schema.default !== undefined) {
     if (Array.isArray(schema.default)) {
       return Object.freeze(schema.default.map((value) => typeof value === 'boolean' ? value : String(value)));
     }
     return typeof schema.default === 'boolean' ? schema.default : String(schema.default);
   }
-  if (schema.type === 'boolean') return false;
+  if (schema.type === 'boolean') return required ? false : undefined;
   if (schema.type === 'array') return Object.freeze([]);
   return '';
 };
 
-export const createRouteInputDraft = (schema: RouteInputSchema): RouteInputDraft => Object.freeze(
-  Object.fromEntries(Object.keys(schema.properties).sort().map((key) => [
-    key,
-    defaultDraftValue(schema.properties[key]!),
-  ])),
-);
+export const createRouteInputDraft = (schema: RouteInputSchema): RouteInputDraft => {
+  const required = new Set(schema.required ?? []);
+  return Object.freeze(Object.fromEntries(
+    Object.keys(schema.properties).sort().flatMap((key) => {
+      const value = defaultDraftValue(schema.properties[key]!, required.has(key));
+      return value === undefined ? [] : [[key, value] as const];
+    }),
+  ));
+};
 
 export const routeInputLabel = (key: string): string => {
   const words = key
@@ -357,7 +368,11 @@ export const cliCommandUsage = (command: RouteManifestCliCommand): string => {
       : `[${option.option}${option.repeated ? '...' : ''}]`);
   const flags = command.options.filter((option) => option.positional === undefined)
     .map((option) => {
-      const value = option.kind === 'boolean' ? `--${option.option}` : `--${option.option} ${cliOperand(option)}`;
+      // Booleans are flags and the grammar rejects boolean arrays, so only
+      // value-carrying options can repeat; ` ...` mirrors cli-entry help rows.
+      const value = option.kind === 'boolean'
+        ? `--${option.option}`
+        : `--${option.option} ${cliOperand(option)}${option.repeated ? ' ...' : ''}`;
       return option.required ? value : `[${value}]`;
     });
   return [...command.path, ...positionals, ...flags].join(' ');
diff --git a/packages/workbench/src/routes/routes-page.tsx b/packages/workbench/src/routes/routes-page.tsx
index 148cb8ed6..537416df6 100644
--- a/packages/workbench/src/routes/routes-page.tsx
+++ b/packages/workbench/src/routes/routes-page.tsx
@@ -77,13 +77,26 @@ const scalarControl = (
   routeId: string,
   key: string,
   schema: Exclude<RouteInputPropertySchema, { readonly type: 'array' }>,
+  required: boolean,
   value: RouteInputDraftValue | undefined,
-  setValue: (value: RouteInputDraftValue) => void,
+  setValue: (value: RouteInputDraftValue | undefined) => void,
 ): React.ReactNode => {
   const id = editorId(routeId, key);
   switch (schema.type) {
     case 'boolean':
-      return <input checked={value === true} id={id} onChange={(event) => setValue(event.currentTarget.checked)} type="checkbox" />;
+      // A checkbox cannot express "unset", so an optional boolean without a
+      // schema default keeps a third omitted state instead of submitting false.
+      return required || schema.default !== undefined
+        ? <input checked={value === true} id={id} onChange={(event) => setValue(event.currentTarget.checked)} type="checkbox" />
+        : <select
+            id={id}
+            onChange={(event) => setValue(event.currentTarget.value === '' ? undefined : event.currentTarget.value === 'true')}
+            value={value === true ? 'true' : value === false ? 'false' : ''}
+          >
+            <option value="">(omitted)</option>
+            <option value="true">true</option>
+            <option value="false">false</option>
+          </select>;
     case 'number':
       return <input id={id} onChange={(event) => setValue(event.currentTarget.value)} type="number" value={typeof value === 'string' ? value : ''} />;
     case 'string':
@@ -123,8 +136,14 @@ const RouteInputEditor = ({ entry, group, onOpenMcp }: {
       ? undefined
       : cliCommandInvocation(entry.command, validated.arguments));
   };
-  const setValue = (key: string, value: RouteInputDraftValue): void => {
-    const next = Object.freeze({ ...draft, [key]: value });
+  const setValue = (key: string, value: RouteInputDraftValue | undefined): void => {
+    const entries = { ...draft };
+    if (value === undefined) {
+      delete entries[key];
+    } else {
+      entries[key] = value;
+    }
+    const next = Object.freeze(entries);
     setDraft(next);
     commitValidation(next);
   };
@@ -181,7 +200,7 @@ const RouteInputEditor = ({ entry, group, onOpenMcp }: {
           if (property.type !== 'array') {
             return <div className="route-input-field" key={key}>
               <label htmlFor={editorId(entry.id, key)}>{label}{required ? ' (required)' : ''}
-                {scalarControl(entry.id, key, property, draft[key], (value) => setValue(key, value))}
+                {scalarControl(entry.id, key, property, required, draft[key], (value) => setValue(key, value))}
               </label>
               {property.description === undefined ? undefined : <p>{property.description}</p>}
               {error === undefined ? undefined : <span className="route-input-error" role="alert">{error}</span>}
@@ -192,7 +211,9 @@ const RouteInputEditor = ({ entry, group, onOpenMcp }: {
             <legend>{label}{required ? ' (required)' : ''}</legend>
             {property.description === undefined ? undefined : <p>{property.description}</p>}
             {values.map((value, index) => <div className="route-input-array-row" key={`${key}-${String(index)}`}>
-              {scalarControl(entry.id, `${key}-${String(index)}`, property.items, value, (nextValue) => {
+              {/* Array rows exist only after "Add", so items are always set. */}
+              {scalarControl(entry.id, `${key}-${String(index)}`, property.items, true, value, (nextValue) => {
+                if (nextValue === undefined) return;
                 const next = [...values];
                 next[index] = nextValue as boolean | string;
                 setValue(key, Object.freeze(next));
diff --git a/packages/workbench/tests/examples-real.e2e.test.ts b/packages/workbench/tests/examples-real.e2e.test.ts
index 9babdb9e8..4c4d6557a 100644
--- a/packages/workbench/tests/examples-real.e2e.test.ts
+++ b/packages/workbench/tests/examples-real.e2e.test.ts
@@ -606,10 +606,10 @@ e2e('renders the flagship compiled route catalog by server and kind in real Chro
     await expect(inventoryTool.getByLabel('Source (required)')).toBeVisible({ timeout: browserTimeout });
     await expect(inventoryTool.getByLabel('Report')).toBeVisible({ timeout: browserTimeout });
     await expect(inventoryTool.getByLabel('Strict')).toBeVisible({ timeout: browserTimeout });
+    await expect(inventoryTool.getByLabel('Strict')).toHaveValue('', { timeout: browserTimeout });
     await inventoryTool.getByRole('button', { name: 'Validate input' }).click();
     await expect(inventoryTool.getByRole('alert')).toHaveText('Source is required.', { timeout: browserTimeout });
     await inventoryTool.getByLabel('Source (required)').fill('/tmp/audiobooks');
-    await inventoryTool.getByLabel('Strict').check();
     await expect(inventoryTool.getByRole('button', { name: 'Open in MCP session' })).toBeEnabled({ timeout: browserTimeout });
     await inventoryTool.getByRole('button', { name: 'Open in MCP session' }).click();
     await waitForSettledWorkbench(page);
@@ -618,7 +618,7 @@ e2e('renders the flagship compiled route catalog by server and kind in real Chro
     const prefill = page.getByRole('status').filter({ hasText: 'Tool call prefilled from Routes' });
     await expect(prefill).toContainText('inventory_sources', { timeout: browserTimeout });
     await expect(prefill).toContainText('"source": "/tmp/audiobooks"', { timeout: browserTimeout });
-    await expect(prefill).toContainText('"strict": true', { timeout: browserTimeout });
+    await expect(prefill).not.toContainText('"strict"', { timeout: browserTimeout });
     await expect(page.getByRole('button', { name: 'Open MCP session' })).toBeEnabled({ timeout: browserTimeout });
     await page.getByRole('link', { name: 'Routes', exact: true }).click();
     await waitForSettledWorkbench(page);
diff --git a/packages/workbench/tests/mcp-page.test.ts b/packages/workbench/tests/mcp-page.test.ts
index 7ef233724..78bdb8ce7 100644
--- a/packages/workbench/tests/mcp-page.test.ts
+++ b/packages/workbench/tests/mcp-page.test.ts
@@ -462,6 +462,33 @@ describe('MCP page', () => {
     expect(markup).toContain('weather');
     expect(markup).toContain('Berlin');
     expect(markup).toContain('Call weather');
+    expect(markup).not.toContain('no longer advertises');
+    expect(pageController.history).toHaveLength(1);
+  });
+
+  it('rejects a stale Routes-page tool prefill without selecting another tool', () => {
+    const pageController = controller();
+    const readyPageController: McpPageController = {
+      ...pageController,
+      model: { ...model, phase: 'ready' } as McpBrowserSessionModel,
+    };
+    const markup = renderToStaticMarkup(createElement(McpPage, {
+      controller: readyPageController,
+      epochOptions: ['epoch-1'],
+      initialBinding: { epochId: 'epoch-1', serverName: 'weather', target: 'codex' },
+      initialToolPrefill: {
+        arguments: { city: 'Berlin' },
+        serverName: 'weather',
+        toolName: 'retired_weather',
+      },
+      serverOptions: [{ name: 'weather', target: 'codex' }],
+      targetOptions: ['codex'],
+    }));
+
+    expect(markup).toContain('The server no longer advertises the &quot;retired_weather&quot; tool.');
+    expect(markup).not.toContain('id="mcp-tool-arguments"');
+    expect(markup).not.toContain('Call weather');
+    expect(markup).not.toContain('Call clock');
     expect(pageController.history).toHaveLength(1);
   });
 
diff --git a/packages/workbench/tests/routes-model.test.ts b/packages/workbench/tests/routes-model.test.ts
index a747532fd..2885aa368 100644
--- a/packages/workbench/tests/routes-model.test.ts
+++ b/packages/workbench/tests/routes-model.test.ts
@@ -1,6 +1,6 @@
 import { expect, it } from '@rstest/core';
 
-import type { RouteManifest } from '../../agent-bundle/src/contracts/routes.ts';
+import type { RouteInputSchema, RouteManifest } from '../../agent-bundle/src/contracts/routes.ts';
 import {
   cliCommandInvocation,
   cliCommandUsage,
@@ -219,6 +219,37 @@ it('prefills projected defaults and validates typed route input before invoke',
   });
 });
 
+it('preserves optional boolean omission while validating explicit and required values', () => {
+  const schema: RouteInputSchema = {
+    additionalProperties: false,
+    properties: {
+      defaulted: { default: true, type: 'boolean' },
+      enabled: { type: 'boolean' },
+      strict: { type: 'boolean' },
+    },
+    required: ['enabled'],
+    type: 'object',
+  };
+  const draft = createRouteInputDraft(schema);
+
+  expect(draft).toEqual({ defaulted: true, enabled: false });
+  expect(validateRouteInput(schema, draft)).toEqual({
+    arguments: { defaulted: true, enabled: false },
+    errors: {},
+  });
+  expect(validateRouteInput(schema, { ...draft, strict: true })).toEqual({
+    arguments: { defaulted: true, enabled: false, strict: true },
+    errors: {},
+  });
+  expect(validateRouteInput(schema, { ...draft, strict: false })).toEqual({
+    arguments: { defaulted: true, enabled: false, strict: false },
+    errors: {},
+  });
+  expect(validateRouteInput(schema, { defaulted: true })).toEqual({
+    errors: { enabled: 'Enabled must be true or false.' },
+  });
+});
+
 it('validates the raw JSON fallback without inventing a schema', () => {
   expect(validateRawRouteInput('{')).toEqual({ error: 'Enter a valid JSON object.' });
   expect(validateRawRouteInput('[]')).toEqual({ error: 'Arguments must be a JSON object.' });
@@ -242,7 +273,7 @@ it('formats CLI usage and a shell-copyable invocation from validated input', ()
   };
 
   expect(cliCommandUsage(command)).toBe(
-    'library audit <input-file> [--format <text|json>] [--tag <string>] [--verbose]',
+    'library audit <input-file> [--format <text|json>] [--tag <string> ...] [--verbose]',
   );
   expect(cliCommandInvocation(command, {
     format: 'json',
@@ -252,6 +283,19 @@ it('formats CLI usage and a shell-copyable invocation from validated input', ()
   })).toBe("library audit '/Audio Books' --format json --tag fiction --tag history --verbose");
 });
 
+it('marks required and optional repeated named flags in CLI usage', () => {
+  expect(cliCommandUsage({
+    aliases: [],
+    exitCode: 'zero',
+    options: [
+      { key: 'source', kind: 'string', option: 'source', repeated: true, required: true },
+      { key: 'tag', kind: 'string', option: 'tag', repeated: true, required: false },
+    ],
+    path: ['library', 'import'],
+    routeId: 'cli:library/import',
+  })).toBe('library import --source <string> ... [--tag <string> ...]');
+});
+
 it('maps a tool route server id and final route segment into an MCP prefill', () => {
   const catalog = routeCatalogFor(manifest);
   const group = catalog.groups[0]!;
diff --git a/packages/workbench/tests/routes-page.test.ts b/packages/workbench/tests/routes-page.test.ts
index 3316055f3..a74a77b9e 100644
--- a/packages/workbench/tests/routes-page.test.ts
+++ b/packages/workbench/tests/routes-page.test.ts
@@ -52,7 +52,9 @@ const manifest: RouteManifest = {
         additionalProperties: false,
         properties: {
           count: { default: 2, description: 'Repeat count.', type: 'number' },
+          enabled: { default: true, type: 'boolean' },
           format: { enum: ['text', 'json'], type: 'string' },
+          strict: { type: 'boolean' },
           tags: { items: { type: 'string' }, type: 'array' },
         },
         required: ['format'],
@@ -145,8 +147,10 @@ it('renders generated fields, descriptions, defaults, required markers, and a ga
   expect(markup).toContain('Generated input editor');
   expect(markup).toContain('Repeat count.');
   expect(markup).toContain('value="2"');
+  expect(markup).toMatch(/Enabled<input[^>]*type="checkbox"[^>]*checked=""/u);
   expect(markup).toContain('Format (required)');
   expect(markup).toContain('<option value="json">json</option>');
+  expect(markup).toMatch(/Strict<select[^>]*><option value=""[^>]*>\(omitted\)<\/option><option value="true">true<\/option><option value="false">false<\/option><\/select>/u);
   expect(markup).toContain('Add Tags item');
   expect(markup).toContain('Full schema validation runs during execution.');
   expect(markup).toContain('Open in MCP session');