diff --git a/server/src/__tests__/github-transport.test.ts b/server/src/__tests__/github-transport.test.ts
new file mode 100644
index 00000000000..9bb65ed0062
--- /dev/null
+++ b/server/src/__tests__/github-transport.test.ts
@@ -0,0 +1,80 @@
+import { generateKeyPairSync } from "node:crypto";
+import { describe, expect, it, vi } from "vitest";
+import { createGitHubAppTransport } from "../services/repository-providers/github-transport.js";
+import { makeGitHubRepository } from "./helpers/fake-github-transport.js";
+
+const privateKey = generateKeyPairSync("rsa", { modulusLength: 2048 })
+  .privateKey.export({ type: "pkcs8", format: "pem" })
+  .toString();
+
+function jsonResponse(body: unknown, status = 200) {
+  return new Response(JSON.stringify(body), {
+    status,
+    headers: { "Content-Type": "application/json" },
+  });
+}
+
+describe("GitHub App transport", () => {
+  it("searches the complete installation catalog before paginating matches", async () => {
+    const repositories = Array.from({ length: 205 }, (_, index) => makeGitHubRepository({
+      id: index + 1,
+      owner: index === 100 || index === 101 || index === 200 ? "matching-owner" : "other-owner",
+      name: `repo-${index + 1}`,
+    }));
+    const fetchImpl = vi.fn(async (input: string | URL | Request) => {
+      const url = new URL(typeof input === "string" ? input : input instanceof URL ? input : input.url);
+      if (url.pathname.endsWith("/access_tokens")) {
+        return jsonResponse({ token: "ghs_test", expires_at: "2099-01-01T00:00:00.000Z" });
+      }
+      const page = Number(url.searchParams.get("page"));
+      const perPage = Number(url.searchParams.get("per_page"));
+      const start = (page - 1) * perPage;
+      return jsonResponse({ total_count: repositories.length, repositories: repositories.slice(start, start + perPage) });
+    });
+    const transport = createGitHubAppTransport({ appId: "1", privateKey, fetchImpl });
+
+    await expect(transport.listRepositories({
+      installationId: "installation-1",
+      page: 1,
+      perPage: 2,
+      query: "matching-owner",
+    })).resolves.toMatchObject({
+      totalCount: 3,
+      items: [{ id: 101 }, { id: 102 }],
+    });
+    await expect(transport.listRepositories({
+      installationId: "installation-1",
+      page: 2,
+      perPage: 2,
+      query: "matching-owner",
+    })).resolves.toMatchObject({
+      totalCount: 3,
+      items: [{ id: 201 }],
+    });
+    expect(fetchImpl.mock.calls.some(([input]) => String(input).includes("per_page=100&page=3"))).toBe(true);
+  });
+
+  it("does not expose provider request paths in operator-facing failures", async () => {
+    const fetchImpl = vi.fn(async (input: string | URL | Request) => {
+      const url = new URL(typeof input === "string" ? input : input instanceof URL ? input : input.url);
+      if (url.pathname.endsWith("/access_tokens")) {
+        return jsonResponse({ token: "ghs_test", expires_at: "2099-01-01T00:00:00.000Z" });
+      }
+      return jsonResponse({ message: "unavailable" }, 503);
+    });
+    const transport = createGitHubAppTransport({ appId: "1", privateKey, fetchImpl });
+
+    await expect(transport.listRepositories({
+      installationId: "sensitive-installation",
+      page: 1,
+      perPage: 20,
+      query: null,
+    })).rejects.toThrow("GitHub repository provider request failed with status 503");
+    await expect(transport.listRepositories({
+      installationId: "sensitive-installation",
+      page: 1,
+      perPage: 20,
+      query: null,
+    })).rejects.not.toThrow("sensitive-installation");
+  });
+});
diff --git a/server/src/__tests__/repositories.test.ts b/server/src/__tests__/repositories.test.ts
index 2648e9054a4..65fab73f117 100644
--- a/server/src/__tests__/repositories.test.ts
+++ b/server/src/__tests__/repositories.test.ts
@@ -533,11 +533,18 @@ describeEmbeddedPostgres("repository services and routes", () => {
       provider: "test_provider",
       sync: async () => ({
         cursor: "cursor-1",
-        repositories: [{
-          providerRepositoryId: "provider-repo-1",
-          cloneUrl: "https://git.example.com/acme/provider-repo.git",
-          visibility: "private",
-        }],
+        repositories: [
+          {
+            providerRepositoryId: "provider-repo-1",
+            cloneUrl: "https://git.example.com/acme/provider-repo-renamed.git",
+            visibility: "private",
+          },
+          {
+            providerRepositoryId: "provider-repo-not-imported",
+            cloneUrl: "https://git.example.com/acme/not-imported.git",
+            visibility: "private",
+          },
+        ],
       }),
       disconnect: async () => {},
     };
@@ -560,9 +567,24 @@ describeEmbeddedPostgres("repository services and routes", () => {
     expect(created.created).toBe(true);
     expect(duplicate.created).toBe(false);
 
+    const providerRepository = await repositoryService(db).upsertProviderRepository(
+      seeded.companyA.id,
+      created.connection.id,
+      provider.provider,
+      {
+        providerRepositoryId: "provider-repo-1",
+        cloneUrl: "https://git.example.com/acme/provider-repo.git",
+        visibility: "private",
+      },
+    );
     const synced = await connections.sync(seeded.companyA.id, created.connection.id);
     expect(synced?.repositories).toHaveLength(1);
-    const providerRepository = synced!.repositories[0]!;
+    expect(synced?.repositories[0]).toMatchObject({
+      id: providerRepository.id,
+      name: "provider-repo-renamed",
+    });
+    expect((await repositoryService(db).list(seeded.companyA.id)).map((repository) => repository.name))
+      .not.toContain("not-imported");
     await repositoryAccessService(db).attachProjectRepository({
       companyId: seeded.companyA.id,
       projectId: seeded.projectOne.id,
diff --git a/server/src/services/repositories.ts b/server/src/services/repositories.ts
index 4bfb1676aba..bdd35931aed 100644
--- a/server/src/services/repositories.ts
+++ b/server/src/services/repositories.ts
@@ -378,5 +378,25 @@ export function repositoryService(db: Db) {
         .returning();
       return rows.map(toRepository);
     },
+
+    markProviderRepositoriesUnavailable: async (
+      companyId: string,
+      connectionId: string,
+      providerRepositoryIds: string[],
+      reason: string,
+    ) => {
+      if (providerRepositoryIds.length === 0) return [];
+      const rows = await db
+        .update(repositories)
+        .set({ state: "unavailable", unavailableReason: reason, updatedAt: new Date() })
+        .where(and(
+          eq(repositories.companyId, companyId),
+          eq(repositories.connectionId, connectionId),
+          inArray(repositories.providerRepositoryId, providerRepositoryIds),
+          ne(repositories.state, "archived"),
+        ))
+        .returning();
+      return rows.map(toRepository);
+    },
   };
 }
diff --git a/server/src/services/repository-connections.ts b/server/src/services/repository-connections.ts
index 556e53a7e18..10a90943152 100644
--- a/server/src/services/repository-connections.ts
+++ b/server/src/services/repository-connections.ts
@@ -1,6 +1,6 @@
 import { and, asc, eq } from "drizzle-orm";
 import type { Db } from "@paperclipai/db";
-import { repositoryConnections } from "@paperclipai/db";
+import { repositoryConnections, repositories } from "@paperclipai/db";
 import type { CreateRepositoryConnection, RepositoryConnection } from "@paperclipai/shared";
 import {
   REPOSITORY_PROVIDER_ANY_HOST,
@@ -337,12 +337,36 @@ export function repositoryConnectionService(
         });
         return await db.transaction(async (tx) => {
           const transactionalRepositories = repositoryService(tx as unknown as Db);
+          const importedRows = await tx
+            .select({ providerRepositoryId: repositories.providerRepositoryId })
+            .from(repositories)
+            .where(and(
+              eq(repositories.companyId, companyId),
+              eq(repositories.connectionId, id),
+            ));
+          const importedIds = new Set(
+            importedRows
+              .map((repository) => repository.providerRepositoryId)
+              .filter((providerRepositoryId): providerRepositoryId is string => Boolean(providerRepositoryId)),
+          );
+          const snapshotsById = new Map(
+            result.repositories.map((snapshot) => [snapshot.providerRepositoryId, snapshot]),
+          );
           const syncedRepositories = [];
-          for (const snapshot of result.repositories) {
+          for (const providerRepositoryId of importedIds) {
+            const snapshot = snapshotsById.get(providerRepositoryId);
+            if (!snapshot) continue;
             syncedRepositories.push(
               await transactionalRepositories.upsertProviderRepository(companyId, id, row.provider, snapshot),
             );
           }
+          const unavailableIds = [...importedIds].filter((providerRepositoryId) => !snapshotsById.has(providerRepositoryId));
+          syncedRepositories.push(...await transactionalRepositories.markProviderRepositoriesUnavailable(
+            companyId,
+            id,
+            unavailableIds,
+            "Repository is no longer available through its provider connection",
+          ));
           const completed = await tx
             .update(repositoryConnections)
             .set({
diff --git a/server/src/services/repository-providers/github-provider.ts b/server/src/services/repository-providers/github-provider.ts
index 93d95c08885..ae9cd70ebb6 100644
--- a/server/src/services/repository-providers/github-provider.ts
+++ b/server/src/services/repository-providers/github-provider.ts
@@ -228,7 +228,10 @@ export function createGitHubProvider(deps: GitHubProviderDeps): RepositoryProvid
         query: input.query?.trim() || null,
       });
       const items = result.items.map(toDiscovered);
-      const nextCursor = items.length === perPage ? String(page + 1) : null;
+      const hasNextPage = result.totalCount !== null
+        ? page * perPage < result.totalCount
+        : items.length === perPage;
+      const nextCursor = hasNextPage ? String(page + 1) : null;
       return { items, nextCursor, total: result.totalCount };
     },
 
diff --git a/server/src/services/repository-providers/github-transport.ts b/server/src/services/repository-providers/github-transport.ts
index 691a3b0c63d..d1ae01f0922 100644
--- a/server/src/services/repository-providers/github-transport.ts
+++ b/server/src/services/repository-providers/github-transport.ts
@@ -68,7 +68,7 @@ export function createGitHubAppTransport(config: GitHubAppTransportConfig): GitH
       },
     });
     if (!response.ok) {
-      throw new Error(`GitHub app request ${path} failed with ${response.status}`);
+      throw new Error(`GitHub App request failed with status ${response.status}`);
     }
     return (await response.json()) as T;
   }
@@ -94,7 +94,7 @@ export function createGitHubAppTransport(config: GitHubAppTransportConfig): GitH
       },
     });
     if (!response.ok) {
-      throw new Error(`GitHub installation request ${path} failed with ${response.status}`);
+      throw new Error(`GitHub repository provider request failed with status ${response.status}`);
     }
     return (await response.json()) as T;
   }
@@ -122,20 +122,40 @@ export function createGitHubAppTransport(config: GitHubAppTransportConfig): GitH
     createInstallationAccessToken,
 
     async listRepositories(input) {
-      const params = new URLSearchParams({ per_page: String(input.perPage), page: String(input.page) });
-      const body = await installationRequest<{ total_count: number; repositories: GitHubRepository[] }>(
-        input.installationId,
-        `/installation/repositories?${params.toString()}`,
-      );
       const query = input.query?.trim().toLowerCase();
       if (!query) {
+        const params = new URLSearchParams({ per_page: String(input.perPage), page: String(input.page) });
+        const body = await installationRequest<{ total_count: number; repositories: GitHubRepository[] }>(
+          input.installationId,
+          `/installation/repositories?${params.toString()}`,
+        );
         return { totalCount: body.total_count ?? null, items: body.repositories ?? [] };
       }
-      // The installation-repositories endpoint has no server-side search; filter
-      // the page client-side. total_count no longer reflects the filtered set.
+
+      // GitHub does not search installation repositories server-side. Walk the
+      // complete installation catalog before paginating so a match on a later
+      // upstream page is neither omitted nor given a misleading next cursor.
+      const matches: GitHubRepository[] = [];
+      let upstreamPage = 1;
+      const upstreamPageSize = 100;
+      for (;;) {
+        const params = new URLSearchParams({
+          per_page: String(upstreamPageSize),
+          page: String(upstreamPage),
+        });
+        const body = await installationRequest<{ total_count: number; repositories: GitHubRepository[] }>(
+          input.installationId,
+          `/installation/repositories?${params.toString()}`,
+        );
+        const pageItems = body.repositories ?? [];
+        matches.push(...pageItems.filter((repo) => repo.full_name.toLowerCase().includes(query)));
+        if (pageItems.length < upstreamPageSize || upstreamPage * upstreamPageSize >= body.total_count) break;
+        upstreamPage += 1;
+      }
+      const start = (input.page - 1) * input.perPage;
       return {
-        totalCount: null,
-        items: (body.repositories ?? []).filter((repo) => repo.full_name.toLowerCase().includes(query)),
+        totalCount: matches.length,
+        items: matches.slice(start, start + input.perPage),
       };
     },