diff --git a/CHANGELOG.md b/CHANGELOG.md
index ccbca3d..0564234 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,12 @@
 # Changelog
 
+## 0.4.1
+
+- Repair stale automatic conversation links when the current project has
+  stronger path or Git evidence.
+- Prevent broad parent repositories from claiming conversations whose recorded
+  Git remote belongs to another project.
+
 ## 0.4.0
 
 - Rename the project and public interfaces to ThreadRelink.
diff --git a/package.json b/package.json
index 7d9bde8..1065521 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "threadrelink-monorepo",
-  "version": "0.4.0",
+  "version": "0.4.1",
   "private": true,
   "description": "Path-independent discovery and recovery for local Codex conversations.",
   "license": "MIT",
diff --git a/packages/core/src/matcher.ts b/packages/core/src/matcher.ts
index 9b1dd70..38a8af9 100644
--- a/packages/core/src/matcher.ts
+++ b/packages/core/src/matcher.ts
@@ -33,35 +33,47 @@ export async function matchThreadToProject(
   context: MatchContext,
 ): Promise<MatchDecision> {
   const { project, existingLink } = context;
-  if (existingLink) {
-    if (existingLink.projectId === project.id) {
-      return decision(
-        thread,
-        "linked",
-        project.id,
-        [
-          {
-            kind: "stored-link",
-            confidence: 1,
-            description: "Conversation was already linked to this ThreadRelink project.",
-          },
-        ],
-        existingLink.relativeCwd,
-      );
-    }
+  if (existingLink?.projectId === project.id) {
+    return decision(
+      thread,
+      "linked",
+      project.id,
+      [
+        {
+          kind: "stored-link",
+          confidence: 1,
+          description: "Conversation was already linked to this ThreadRelink project.",
+        },
+      ],
+      existingLink.relativeCwd,
+    );
+  }
+  if (existingLink?.linkedBy === "manual") {
     return decision(thread, "unlinked", null, [
       {
         kind: "stored-link",
         confidence: 1,
-        description: "Conversation is already linked to another ThreadRelink project.",
+        description:
+          "Conversation was manually linked to another ThreadRelink project.",
       },
     ]);
   }
 
+  const threadRemote = thread.gitInfo?.originUrl
+    ? normalizeRemoteUrl(thread.gitInfo.originUrl)
+    : null;
+  const remoteMatches = Boolean(
+    threadRemote && project.remotes.includes(threadRemote),
+  );
+  const remoteConflicts = Boolean(
+    threadRemote
+    && project.remotes.length > 0
+    && !remoteMatches,
+  );
   const matchingAlias = project.aliases.find((alias) =>
     isPathInside(thread.cwd, alias.path)
   );
-  if (matchingAlias) {
+  if (matchingAlias && !remoteConflicts) {
     return decision(
       thread,
       "linked",
@@ -77,12 +89,6 @@ export async function matchThreadToProject(
     );
   }
 
-  const threadRemote = thread.gitInfo?.originUrl
-    ? normalizeRemoteUrl(thread.gitInfo.originUrl)
-    : null;
-  const remoteMatches = Boolean(
-    threadRemote && project.remotes.includes(threadRemote),
-  );
   const shaMatches = Boolean(
     context.gitRoot
     && thread.gitInfo?.sha
@@ -130,5 +136,16 @@ export async function matchThreadToProject(
     ]);
   }
 
+  if (existingLink) {
+    return decision(thread, "unlinked", null, [
+      {
+        kind: "stored-link",
+        confidence: 1,
+        description:
+          "Conversation has an automatic link to another ThreadRelink project and no stronger evidence was found.",
+      },
+    ]);
+  }
+
   return decision(thread, "unlinked", null, []);
 }
diff --git a/packages/core/test/matcher.test.ts b/packages/core/test/matcher.test.ts
index 85807f4..9e22da4 100644
--- a/packages/core/test/matcher.test.ts
+++ b/packages/core/test/matcher.test.ts
@@ -2,6 +2,7 @@ import { describe, expect, it } from "vitest";
 import { matchThreadToProject } from "../src/matcher.js";
 import type {
   ProjectRecord,
+  ThreadLink,
   ThreadMetadata,
 } from "../src/types.js";
 
@@ -45,6 +46,27 @@ function thread(overrides: Partial<ThreadMetadata> = {}): ThreadMetadata {
   };
 }
 
+function link(overrides: Partial<ThreadLink> = {}): ThreadLink {
+  return {
+    provider: "codex",
+    threadId: "thread-1",
+    projectId: "project-old",
+    linkedBy: "automatic",
+    originalCwd: "/repo/ToolSpec",
+    relativeCwd: "",
+    evidence: [
+      {
+        kind: "path-alias",
+        confidence: 1,
+        description: "Legacy automatic path match.",
+      },
+    ],
+    createdAt: "2026-01-01T00:00:00.000Z",
+    updatedAt: "2026-01-01T00:00:00.000Z",
+    ...overrides,
+  };
+}
+
 describe("conversation matching", () => {
   it("automatically links a known historical path alias", async () => {
     const result = await matchThreadToProject(thread(), {
@@ -102,4 +124,52 @@ describe("conversation matching", () => {
     expect(result.status).toBe("suggested");
     expect(result.evidence[0]?.confidence).toBeLessThan(0.9);
   });
+
+  it("repairs an automatic link to another project when a path alias matches", async () => {
+    const result = await matchThreadToProject(thread(), {
+      project,
+      existingLink: link(),
+      gitRoot: "/repo/FinSpec",
+      shaExists: async () => false,
+    });
+
+    expect(result.status).toBe("linked");
+    expect(result.projectId).toBe(project.id);
+    expect(result.evidence[0]?.kind).toBe("path-alias");
+  });
+
+  it("does not automatically replace a manual link to another project", async () => {
+    const result = await matchThreadToProject(thread(), {
+      project,
+      existingLink: link({ linkedBy: "manual" }),
+      gitRoot: "/repo/FinSpec",
+      shaExists: async () => false,
+    });
+
+    expect(result.status).toBe("unlinked");
+    expect(result.projectId).toBeNull();
+    expect(result.evidence[0]?.description).toContain("manually linked");
+  });
+
+  it("rejects a broad path alias when the recorded Git remote conflicts", async () => {
+    const result = await matchThreadToProject(
+      thread({
+        cwd: "/repo/ToolSpec/nested-project",
+        gitInfo: {
+          branch: "main",
+          originUrl: "https://github.com/ascendho/other-project.git",
+          sha: null,
+        },
+      }),
+      {
+        project,
+        existingLink: null,
+        gitRoot: "/repo/FinSpec",
+        shaExists: async () => false,
+      },
+    );
+
+    expect(result.status).toBe("unlinked");
+    expect(result.projectId).toBeNull();
+  });
 });
diff --git a/packages/core/test/service.test.ts b/packages/core/test/service.test.ts
index 9165905..711ac03 100644
--- a/packages/core/test/service.test.ts
+++ b/packages/core/test/service.test.ts
@@ -159,6 +159,81 @@ describe("ThreadRelinkService", () => {
       .toEqual(expect.arrayContaining([oldRoot, newRoot]));
   });
 
+  it("moves a stale automatic link when the current project has stronger evidence", async () => {
+    const base = await mkdtemp(join(tmpdir(), "threadrelink-stale-link-"));
+    cleanup.push(base);
+    const root = join(base, "internship-notes");
+    const registryHome = join(base, "state");
+    await mkdir(root);
+    await execFileAsync("git", ["init", root]);
+
+    const conversation: ThreadMetadata = {
+      provider: "codex",
+      id: "thread-stale-parent",
+      name: "Internship notes",
+      preview: "Internship notes",
+      cwd: root,
+      createdAt: 1,
+      updatedAt: 2,
+      archived: false,
+      cliVersion: "0.145.0",
+      modelProvider: "openai",
+      gitInfo: null,
+    };
+    const service = new ThreadRelinkService({
+      registryHome,
+      historyAdapterFactory: async () => adapterFor([conversation]),
+      now: () => new Date("2026-07-28T00:00:00.000Z"),
+    });
+    const currentProject = await service.initProject(root);
+    const originalCreatedAt = "2026-07-27T00:00:00.000Z";
+    await service.registry.update((draft) => {
+      draft.projects.push({
+        id: "legacy-parent",
+        name: "home",
+        kind: "git",
+        aliases: [{
+          path: base,
+          key: base,
+          firstSeenAt: originalCreatedAt,
+          lastSeenAt: originalCreatedAt,
+        }],
+        remotes: [],
+        createdAt: originalCreatedAt,
+        updatedAt: originalCreatedAt,
+      });
+      draft.threadLinks.push({
+        provider: "codex",
+        threadId: conversation.id,
+        projectId: "legacy-parent",
+        linkedBy: "automatic",
+        originalCwd: conversation.cwd,
+        relativeCwd: "internship-notes",
+        evidence: [{
+          kind: "path-alias",
+          confidence: 1,
+          description: "Legacy parent path match.",
+        }],
+        createdAt: originalCreatedAt,
+        updatedAt: originalCreatedAt,
+      });
+    });
+
+    const result = await service.sync(root);
+    const repairedLink = (await service.registry.read()).threadLinks.find(
+      (candidate) => candidate.threadId === conversation.id,
+    );
+
+    expect(result.linked.map((item) => item.thread.id))
+      .toContain(conversation.id);
+    expect(repairedLink).toMatchObject({
+      projectId: currentProject.id,
+      linkedBy: "automatic",
+      createdAt: originalCreatedAt,
+      evidence: [{ kind: "path-alias" }],
+    });
+  });
+
   it("persists an explicit relink for an otherwise unverifiable move", async () => {
     const base = await mkdtemp(join(tmpdir(), "threadrelink-relink-"));
     cleanup.push(base);
diff --git a/packages/vscode/CHANGELOG.md b/packages/vscode/CHANGELOG.md
index 93b715f..6197a70 100644
--- a/packages/vscode/CHANGELOG.md
+++ b/packages/vscode/CHANGELOG.md
@@ -1,5 +1,12 @@
 # Changelog
 
+## 0.4.1
+
+- Repair stale automatic conversation links when the current project has
+  stronger path or Git evidence.
+- Preserve manual links while preventing broad parent repositories from
+  claiming conversations with conflicting Git remotes.
+
 ## 0.4.0
 
 - Rename the project and public interfaces to ThreadRelink.
diff --git a/packages/vscode/package.json b/packages/vscode/package.json
index 01df338..0ce3a71 100644
--- a/packages/vscode/package.json
+++ b/packages/vscode/package.json
@@ -2,7 +2,7 @@
   "name": "threadrelink",
   "displayName": "ThreadRelink",
   "description": "A VS Code extension that keeps local Codex conversations discoverable after a repository is renamed or moved.",
-  "version": "0.4.0",
+  "version": "0.4.1",
   "icon": "resources/threadrelink.png",
   "publisher": "ascendho",
   "repository": {