diff --git a/src/signals/onboarding-pack.ts b/src/signals/onboarding-pack.ts
index c36fb904f1..4d7b34ed95 100644
--- a/src/signals/onboarding-pack.ts
+++ b/src/signals/onboarding-pack.ts
@@ -1,4 +1,5 @@
 import { isFocusManifestPublicSafe, type FocusManifestPolicy } from "./focus-manifest";
+import { labelPolicyNote } from "./repo-policy-compiler";
 import { nowIso } from "../utils/json";
 
 export type RepoPolicyContributionLane = {
@@ -99,6 +100,7 @@ export function focusManifestPolicyToCompilerOutput(policy: FocusManifestPolicy)
       preferredLabels: policy.publicSafe.labelPolicy.preferredLabels,
       requiredLabels: [],
       discouragedLabels: [],
+      note: labelPolicyNote(policy.publicSafe.validation.linkedIssuePolicy),
     },
     validationExpectations: policy.publicSafe.validation.expectations,
     readinessWarnings: policy.publicSafe.readinessWarnings,
diff --git a/src/signals/repo-policy-compiler.ts b/src/signals/repo-policy-compiler.ts
index 3de715f1f7..78c96a6134 100644
--- a/src/signals/repo-policy-compiler.ts
+++ b/src/signals/repo-policy-compiler.ts
@@ -112,7 +112,10 @@ function issueDiscoverySummary(preference: FocusManifestLanePreference, summary:
   return "Issue discovery is optional; confirm maintainer scope before filing new issues.";
 }
 
-function labelPolicyNote(linkedIssuePolicy: string): string {
+/** Shared by {@link focusManifestPolicyToCompilerOutput} (onboarding-pack.ts) so both adapters compile the same
+ *  manifest to the same `labelPolicy.note` (#5943). The reverse import there is type-only and erased, so this
+ *  export introduces no runtime cycle. */
+export function labelPolicyNote(linkedIssuePolicy: string): string {
   if (linkedIssuePolicy === "required") return "Link a tracked issue before opening a pull request.";
   if (linkedIssuePolicy === "preferred") return "Link a tracked issue when one exists.";
   return "Use labels to explain accepted scope, not to promise outcomes.";
diff --git a/test/unit/onboarding-pack.test.ts b/test/unit/onboarding-pack.test.ts
index a4d6be41d5..2d8f90f38c 100644
--- a/test/unit/onboarding-pack.test.ts
+++ b/test/unit/onboarding-pack.test.ts
@@ -5,10 +5,11 @@ import {
 } from "../../src/services/repo-onboarding-pack";
 import { createTestEnv } from "../helpers/d1";
 import { upsertRepositoryFromGitHub } from "../../src/db/repositories";
-import { parseFocusManifestContent } from "../../src/signals/focus-manifest";
+import { compileFocusManifestPolicy, parseFocusManifest, parseFocusManifestContent } from "../../src/signals/focus-manifest";
 import { compileRepoPolicyCompilerOutput } from "../../src/signals/repo-policy-compiler";
 import {
   buildRepoOnboardingPackPreview,
+  focusManifestPolicyToCompilerOutput,
   isRepoOnboardingPackPublicSafe,
   type RepoPolicyCompilerOutput,
 } from "../../src/signals/onboarding-pack";
@@ -264,6 +265,42 @@ describe("buildRepoOnboardingPackPreview", () => {
   });
 });
 
+// Both adapters compile the SAME FocusManifest into the same RepoPolicyCompilerOutput.labelPolicy shape, so they
+// must not disagree on any field: focusManifestPolicyToCompilerOutput omitted `note` entirely (#5943), silently
+// dropping the linked-issue guidance from registration-readiness's onboardingPackPreview while the direct
+// onboarding-pack API/MCP path (compileRepoPolicyCompilerOutput) kept it.
+describe("focusManifestPolicyToCompilerOutput labelPolicy.note parity (#5943)", () => {
+  const GENERATED_AT = "2026-06-02T12:00:00.000Z";
+
+  it.each([
+    ["required", /tracked issue before opening/i],
+    ["preferred", /when one exists/i],
+    ["optional", /accepted scope/i],
+  ] as const)("linkedIssuePolicy %s yields the same non-null note as compileRepoPolicyCompilerOutput", (linkedIssuePolicy, expected) => {
+    const manifest = parseFocusManifest({ wantedPaths: ["src/"], linkedIssuePolicy });
+    const fromAdapter = focusManifestPolicyToCompilerOutput(
+      compileFocusManifestPolicy("owner/repo", manifest, { generatedAt: GENERATED_AT }),
+    );
+    const fromCompiler = compileRepoPolicyCompilerOutput({ repoFullName: "owner/repo", manifest, generatedAt: GENERATED_AT });
+
+    expect(fromAdapter.labelPolicy?.note).toEqual(expect.any(String));
+    expect(fromAdapter.labelPolicy?.note).toMatch(expected);
+    expect(fromAdapter.labelPolicy?.note).toBe(fromCompiler.labelPolicy?.note);
+  });
+
+  it("leaves every other labelPolicy field untouched (the fix is scoped to note)", () => {
+    const manifest = parseFocusManifest({ wantedPaths: ["src/"], preferredLabels: ["bug"], linkedIssuePolicy: "required" });
+    const output = focusManifestPolicyToCompilerOutput(compileFocusManifestPolicy("owner/repo", manifest, { generatedAt: GENERATED_AT }));
+
+    expect(output.labelPolicy).toEqual({
+      preferredLabels: ["bug"],
+      requiredLabels: [],
+      discouragedLabels: [],
+      note: "Link a tracked issue before opening a pull request.",
+    });
+  });
+});
+
 describe("buildRepoOnboardingPackPreviewForRepo", () => {
   it("returns preview_only pack for an installed repo", async () => {
     const env = createTestEnv();
diff --git a/test/unit/registration-readiness.test.ts b/test/unit/registration-readiness.test.ts
index d82da7076c..8feebaf214 100644
--- a/test/unit/registration-readiness.test.ts
+++ b/test/unit/registration-readiness.test.ts
@@ -308,6 +308,32 @@ describe("buildRegistrationReadiness", () => {
     expect(JSON.stringify(report.onboardingPackPreview)).not.toMatch(FORBIDDEN_PUBLIC_LANGUAGE);
   });
 
+  // #5943: focusManifestPolicyToCompilerOutput dropped labelPolicy.note, so this preview always rendered
+  // note: null — silently losing the linked-issue guidance the same manifest produces via the direct
+  // onboarding-pack API/MCP path (compileRepoPolicyCompilerOutput).
+  it("onboardingPackPreview surfaces labelPolicy.note from the manifest's linkedIssuePolicy (#5943)", () => {
+    const repo = repoFor("octo/note", configFor({ repo: "octo/note" }));
+    const readinessFor = (linkedIssuePolicy: "required" | "preferred" | "optional") =>
+      buildRegistrationReadiness({
+        repoFullName: repo.fullName,
+        repo,
+        settings: settingsFor(repo.fullName),
+        installation: healthyInstall,
+        ...signalsFor(repo, [], [], [label("bug")]),
+        focusManifest: parseFocusManifest({ wantedPaths: ["src/signals/"], linkedIssuePolicy }),
+      });
+
+    expect(readinessFor("required").onboardingPackPreview?.labelPolicy.note).toBe(
+      "Link a tracked issue before opening a pull request.",
+    );
+    expect(readinessFor("preferred").onboardingPackPreview?.labelPolicy.note).toBe(
+      "Link a tracked issue when one exists.",
+    );
+    expect(readinessFor("optional").onboardingPackPreview?.labelPolicy.note).toBe(
+      "Use labels to explain accepted scope, not to promise outcomes.",
+    );
+  });
+
   it("onboardingPackPreview strips unsafe public notes via the policy compiler pipeline", () => {
     const repo = repoFor("octo/unsafe", configFor({ repo: "octo/unsafe" }));
     const report = buildRegistrationReadiness({