diff --git a/server/src/__tests__/tool-access-service.test.ts b/server/src/__tests__/tool-access-service.test.ts
index 0d6e1e4fe20..bac38f91298 100644
--- a/server/src/__tests__/tool-access-service.test.ts
+++ b/server/src/__tests__/tool-access-service.test.ts
@@ -7140,6 +7140,25 @@ describeEmbeddedPostgres("tool access service", () => {
     expect(audits).toHaveLength(2);
     expect(audits.every((audit) => audit.actorType === "user" && audit.actorId === member.userId)).toBe(true);
   });
+
+  it("removes orphaned agent installs during replacement", async () => {
+    const company = await createCompany(db);
+    const agent = await createAgent(db, company.id);
+    const { connection } = await createRemoteToolFixture(db, company.id);
+    const service = toolAccessService(db);
+    await service.putConnectionInstalls(connection.id, {
+      installs: [{ targetType: "agent", targetId: agent.id }],
+    });
+    await db.delete(agents).where(eq(agents.id, agent.id));
+
+    const response = await request(createRouteApp(db))
+      .put(`/api/tool-connections/${connection.id}/installs`)
+      .send({ installs: [] });
+
+    expect(response.status).toBe(200);
+    expect(response.body).toMatchObject({ connectionId: connection.id, installs: [] });
+    await expect(db.select().from(toolConnectionInstalls)).resolves.toEqual([]);
+  });
 });
 
 describe("classifyRisk", () => {
diff --git a/server/src/routes/tool-access.ts b/server/src/routes/tool-access.ts
index dcfc4d49b75..2df274da93b 100644
--- a/server/src/routes/tool-access.ts
+++ b/server/src/routes/tool-access.ts
@@ -733,12 +733,16 @@ export function toolAccessRoutes(
             .map((install) => install.targetId),
         )];
         for (const agentId of changedAgentIds) {
+          const installKey = `agent:${agentId}`;
           const [agent] = await db
             .select({ id: agents.id, companyId: agents.companyId })
             .from(agents)
             .where(and(eq(agents.id, agentId), eq(agents.companyId, connection.companyId)))
             .limit(1);
-          if (!agent) throw forbidden("The target agent is not available in this company");
+          if (!agent) {
+            if (!requestedKeys.has(installKey)) continue;
+            throw forbidden("The target agent is not available in this company");
+          }
           const decision = await access.decide({
             actor: req.actor,
             action: "agent_config:update",