diff --git a/packages/core/src/agents/registry.test.ts b/packages/core/src/agents/registry.test.ts
index 7618440957..f57ce9f5d6 100644
--- a/packages/core/src/agents/registry.test.ts
+++ b/packages/core/src/agents/registry.test.ts
@@ -1011,44 +1011,57 @@ describe('AgentRegistry', () => {
       );
     });
 
-    it('should overwrite an existing agent definition', async () => {
+    it('should override an existing agent but warn on duplicate name', async () => {
       await registry.testRegisterAgent(MOCK_AGENT_V1);
       expect(registry.getDefinition('MockAgent')?.description).toBe(
         'Mock Description V1',
       );
 
+      const feedbackSpy = vi.spyOn(coreEvents, 'emitFeedback');
       await registry.testRegisterAgent(MOCK_AGENT_V2);
+
+      // Should override to V2 (preserves existing precedence)
       expect(registry.getDefinition('MockAgent')?.description).toBe(
         'Mock Description V2 (Updated)',
       );
       expect(registry.getAllDefinitions()).toHaveLength(1);
+      // But should emit a warning about the duplicate
+      expect(feedbackSpy).toHaveBeenCalledWith(
+        'warning',
+        expect.stringContaining("Duplicate agent name 'MockAgent'"),
+      );
     });
 
-    it('should log overwrites when in debug mode', async () => {
+    it('should not warn when re-registering the same definition (refresh)', async () => {
+      await registry.testRegisterAgent(MOCK_AGENT_V1);
+      expect(registry.getDefinition('MockAgent')?.description).toBe(
+        'Mock Description V1',
+      );
+
+      // Re-registering the exact same object should succeed without warning
+      const feedbackSpy = vi.spyOn(coreEvents, 'emitFeedback');
+      await registry.testRegisterAgent(MOCK_AGENT_V1);
+      expect(registry.getDefinition('MockAgent')?.description).toBe(
+        'Mock Description V1',
+      );
+      expect(feedbackSpy).not.toHaveBeenCalledWith(
+        'warning',
+        expect.stringContaining('Duplicate'),
+      );
+    });
+
+    it('should warn on duplicate in debug logs', async () => {
       const debugConfig = makeMockedConfig({ debugMode: true });
       const debugRegistry = new TestableAgentRegistry(debugConfig);
-      const debugLogSpy = vi
-        .spyOn(debugLogger, 'log')
+      const warnSpy = vi
+        .spyOn(debugLogger, 'warn')
         .mockImplementation(() => {});
 
       await debugRegistry.testRegisterAgent(MOCK_AGENT_V1);
       await debugRegistry.testRegisterAgent(MOCK_AGENT_V2);
 
-      expect(debugLogSpy).toHaveBeenCalledWith(
-        `[AgentRegistry] Overriding agent 'MockAgent'`,
-      );
-    });
-
-    it('should not log overwrites when not in debug mode', async () => {
-      const debugLogSpy = vi
-        .spyOn(debugLogger, 'log')
-        .mockImplementation(() => {});
-
-      await registry.testRegisterAgent(MOCK_AGENT_V1);
-      await registry.testRegisterAgent(MOCK_AGENT_V2);
-
-      expect(debugLogSpy).not.toHaveBeenCalledWith(
-        `[AgentRegistry] Overriding agent 'MockAgent'`,
+      expect(warnSpy).toHaveBeenCalledWith(
+        expect.stringContaining('Overriding agent'),
       );
     });
 
diff --git a/packages/core/src/agents/registry.ts b/packages/core/src/agents/registry.ts
index b9d434e4c7..7264ad7b92 100644
--- a/packages/core/src/agents/registry.ts
+++ b/packages/core/src/agents/registry.ts
@@ -328,14 +328,28 @@ export class AgentRegistry {
   }
 
   /**
-   * Registers an agent definition. If an agent with the same name exists,
-   * it will be overwritten, respecting the precedence established by the
-   * initialization order.
+   * Registers an agent definition. If an agent with the same name already
+   * exists from a different definition, a warning is emitted to surface
+   * potential state collision. The new definition still overwrites the old
+   * one to preserve existing precedence order (user → project → extension).
    */
   protected async registerAgent<TOutput extends z.ZodTypeAny>(
     definition: AgentDefinition<TOutput>,
     errors?: string[],
   ): Promise<void> {
+    const existing = this.agents.get(definition.name);
+    if (existing && existing !== definition) {
+      coreEvents.emitFeedback(
+        'warning',
+        `Duplicate agent name '${definition.name}' detected. ` +
+          `The later definition will override the earlier one. ` +
+          `Rename one of the agents to avoid this conflict.`,
+      );
+      debugLogger.warn(
+        `[AgentRegistry] Overriding agent '${definition.name}' — duplicate name from a different definition.`,
+      );
+    }
+
     if (definition.kind === 'local') {
       this.registerLocalAgent(definition);
     } else if (definition.kind === 'remote') {
diff --git a/packages/core/src/agents/remote-session-invocation.test.ts b/packages/core/src/agents/remote-session-invocation.test.ts
index d611dd7399..3811c47627 100644
--- a/packages/core/src/agents/remote-session-invocation.test.ts
+++ b/packages/core/src/agents/remote-session-invocation.test.ts
@@ -215,7 +215,7 @@ describe('RemoteSessionInvocation', () => {
     it('should pass initial state from static map to session', async () => {
       const priorState = { contextId: 'ctx-42', taskId: 'task-42' };
 
-      // Seed the static map before constructing the invocation
+      // Seed the static map before constructing the invocation (composite key)
       (
         RemoteSessionInvocation as unknown as {
           sessionState: Map<string, unknown>;
@@ -257,7 +257,7 @@ describe('RemoteSessionInvocation', () => {
         abortSignal: new AbortController().signal,
       });
 
-      // Verify the state was persisted in the static map
+      // Verify the state was persisted in the static map (composite key)
       const storedState = (
         RemoteSessionInvocation as unknown as {
           sessionState: Map<string, { contextId?: string; taskId?: string }>;