diff --git a/src/lib/github-affiliation.test.ts b/src/lib/github-affiliation.test.ts
index dca5f44..c977f5d 100644
--- a/src/lib/github-affiliation.test.ts
+++ b/src/lib/github-affiliation.test.ts
@@ -39,37 +39,62 @@ function makeOctokit() {
 }
 
 describe("getGithubRepositories - affiliation", () => {
-  test("defaults to owner+collaborator when field is unset (backward compat)", async () => {
+  test("defaults to owner+collaborator+organization_member when field is unset (backward compat)", async () => {
     const { octokit, getCaptured } = makeOctokit();
     await getGithubRepositories({ octokit, config: { githubConfig: { owner: "octo" } as any } });
-    expect(getCaptured()?.affiliation).toBe("owner,collaborator");
+    expect(getCaptured()?.affiliation).toBe("owner,collaborator,organization_member");
   });
 
-  test("uses owner only when includeCollaboratorRepos is false", async () => {
+  test("uses owner+organization_member when includeCollaboratorRepos is false", async () => {
     const { octokit, getCaptured } = makeOctokit();
     await getGithubRepositories({
       octokit,
       config: { githubConfig: { owner: "octo", includeCollaboratorRepos: false } as any },
     });
-    expect(getCaptured()?.affiliation).toBe("owner");
+    expect(getCaptured()?.affiliation).toBe("owner,organization_member");
   });
 
-  test("uses owner+collaborator when includeCollaboratorRepos is true", async () => {
+  test("uses owner+collaborator+organization_member when includeCollaboratorRepos is true", async () => {
     const { octokit, getCaptured } = makeOctokit();
     await getGithubRepositories({
       octokit,
       config: { githubConfig: { owner: "octo", includeCollaboratorRepos: true } as any },
     });
-    expect(getCaptured()?.affiliation).toBe("owner,collaborator");
+    expect(getCaptured()?.affiliation).toBe("owner,collaborator,organization_member");
   });
 
-  test("override forces owner+collaborator regardless of config (used by cleanup)", async () => {
+  test("override forces owner+collaborator+organization_member regardless of config (used by cleanup)", async () => {
     const { octokit, getCaptured } = makeOctokit();
     await getGithubRepositories({
       octokit,
       config: { githubConfig: { owner: "octo", includeCollaboratorRepos: false } as any },
       includeCollaboratorReposOverride: true,
     });
-    expect(getCaptured()?.affiliation).toBe("owner,collaborator");
+    expect(getCaptured()?.affiliation).toBe("owner,collaborator,organization_member");
+  });
+
+  test("always includes organization_member (regression guard for org-repo invisibility)", async () => {
+    const cases: Array<{ includeCollab?: boolean; override?: boolean }> = [
+      {},
+      { includeCollab: true },
+      { includeCollab: false },
+      { override: true },
+      { includeCollab: false, override: true },
+    ];
+    for (const c of cases) {
+      const { octokit, getCaptured } = makeOctokit();
+      await getGithubRepositories({
+        octokit,
+        config: {
+          githubConfig: {
+            owner: "octo",
+            ...(c.includeCollab !== undefined && { includeCollaboratorRepos: c.includeCollab }),
+          } as any,
+        },
+        ...(c.override !== undefined && { includeCollaboratorReposOverride: c.override }),
+      });
+      const aff = String(getCaptured()?.affiliation ?? "");
+      expect(aff.split(",")).toContain("organization_member");
+    }
   });
 });
diff --git a/src/lib/github.ts b/src/lib/github.ts
index 680a54e..a1507e3 100644
--- a/src/lib/github.ts
+++ b/src/lib/github.ts
@@ -249,7 +249,13 @@ export async function getGithubRepositories({
       includeCollaboratorReposOverride ??
       config.githubConfig?.includeCollaboratorRepos ??
       true;
-    const affiliation = includeCollab ? "owner,collaborator" : "owner";
+    // Always include organization_member so repos owned by orgs the user
+    // belongs to are returned. Omitting it caused org repos to be invisible
+    // to the main sync, the scheduler, and the cleanup service (which then
+    // archived them on restart as if they had been deleted on GitHub).
+    const affiliation = includeCollab
+      ? "owner,collaborator,organization_member"
+      : "owner,organization_member";
 
     const repos = await octokit.paginate(
       octokit.repos.listForAuthenticatedUser,