diff --git a/src/main/AryxAppService.ts b/src/main/AryxAppService.ts
index 561b343..7bbb30b 100644
--- a/src/main/AryxAppService.ts
+++ b/src/main/AryxAppService.ts
@@ -2348,8 +2348,10 @@ export class AryxAppService extends EventEmitter<AppServiceEvents> {
     left?: DiscoveredToolingState,
     right?: DiscoveredToolingState,
   ): boolean {
-    return JSON.stringify(normalizeDiscoveredToolingState(left).mcpServers)
-      === JSON.stringify(normalizeDiscoveredToolingState(right).mcpServers);
+    const stripRuntime = (servers: DiscoveredMcpServer[]) =>
+      servers.map(({ probedTools: _, ...rest }) => rest);
+    return JSON.stringify(stripRuntime(normalizeDiscoveredToolingState(left).mcpServers))
+      === JSON.stringify(stripRuntime(normalizeDiscoveredToolingState(right).mcpServers));
   }
 
   private equalProjectCustomizationState(
diff --git a/src/shared/domain/discoveredTooling.ts b/src/shared/domain/discoveredTooling.ts
index 8c5874f..65fc860 100644
--- a/src/shared/domain/discoveredTooling.ts
+++ b/src/shared/domain/discoveredTooling.ts
@@ -122,6 +122,7 @@ export function mergeDiscoveredToolingState(
         return {
           ...server,
           status: existing.status,
+          probedTools: existing.probedTools,
         } satisfies DiscoveredMcpServer;
       }
 
diff --git a/tests/shared/discoveredTooling.test.ts b/tests/shared/discoveredTooling.test.ts
index 9c9c18c..5521dd9 100644
--- a/tests/shared/discoveredTooling.test.ts
+++ b/tests/shared/discoveredTooling.test.ts
@@ -105,4 +105,50 @@ describe('discovered tooling helpers', () => {
     expect(listPendingDiscoveredMcpServers(dismissed)).toEqual([]);
     expect(dismissed.mcpServers[1]?.status).toBe('dismissed');
   });
+
+  test('preserves probedTools when fingerprint is unchanged on re-scan', () => {
+    const probedTools = [
+      { name: 'git_status', description: 'Get git status' },
+      { name: 'git_diff', description: 'Get git diff' },
+    ];
+    const current = {
+      mcpServers: [
+        createDiscoveredServer({
+          status: 'accepted',
+          probedTools,
+        }),
+      ],
+      lastScannedAt: TIMESTAMP,
+    };
+
+    const merged = mergeDiscoveredToolingState(
+      current,
+      [createDiscoveredServer()],
+      '2026-03-25T01:00:00.000Z',
+    );
+
+    expect(merged.mcpServers[0]?.probedTools).toEqual(probedTools);
+    expect(merged.mcpServers[0]?.status).toBe('accepted');
+  });
+
+  test('drops probedTools when fingerprint changes on re-scan', () => {
+    const current = {
+      mcpServers: [
+        createDiscoveredServer({
+          status: 'accepted',
+          probedTools: [{ name: 'git_status' }],
+        }),
+      ],
+      lastScannedAt: TIMESTAMP,
+    };
+
+    const merged = mergeDiscoveredToolingState(
+      current,
+      [createDiscoveredServer({ args: ['server.js', '--debug'] })],
+      '2026-03-25T01:00:00.000Z',
+    );
+
+    expect(merged.mcpServers[0]?.probedTools).toBeUndefined();
+    expect(merged.mcpServers[0]?.status).toBe('pending');
+  });
 });