diff --git a/apps/desktop/src/app/chat/runtime-repository.test.ts b/apps/desktop/src/app/chat/runtime-repository.test.ts
new file mode 100644
index 00000000000..d7eec0e34f0
--- /dev/null
+++ b/apps/desktop/src/app/chat/runtime-repository.test.ts
@@ -0,0 +1,58 @@
+import { MessageRepository } from '@assistant-ui/core/internal'
+import { renderHook } from '@testing-library/react'
+import { describe, expect, it } from 'vitest'
+
+import type { ChatMessage } from '@/lib/chat-messages'
+import { syncRepositoryIncrementally } from '@/lib/incremental-external-store-runtime'
+
+import { useRuntimeMessageRepository } from './runtime-repository'
+
+const text = (id: string, role: ChatMessage['role'], body: string): ChatMessage => ({
+  id,
+  role,
+  parts: [{ type: 'text', text: body }]
+})
+
+/** The repository the runtime drives — it throws on a duplicate link. */
+const feedToRepository = (repository: ExportedRepository) => {
+  const runtime = { repository: new MessageRepository() } as unknown as Parameters<
+    typeof syncRepositoryIncrementally
+  >[0]
+
+  return syncRepositoryIncrementally(runtime, repository)
+}
+
+type ExportedRepository = ReturnType<typeof useRuntimeMessageRepository>
+
+describe('useRuntimeMessageRepository', () => {
+  it('emits each id once when the transcript repeats one', () => {
+    const { result } = renderHook(() =>
+      useRuntimeMessageRepository([
+        text('user-1', 'user', 'hi'),
+        text('assistant-1', 'assistant', 'hello'),
+        text('user-1', 'user', 'hi')
+      ])
+    )
+
+    const ids = result.current.messages.map(item => item.message.id)
+
+    expect(ids).toEqual(['user-1', 'assistant-1'])
+  })
+
+  it('builds a repository the runtime can link without throwing', () => {
+    const { result } = renderHook(() =>
+      useRuntimeMessageRepository([
+        text('user-1', 'user', 'hi'),
+        text('assistant-stream-1', 'assistant', 'partial'),
+        text('assistant-stream-1', 'assistant', 'partial'),
+        text('user-2', 'user', 'more')
+      ])
+    )
+
+    expect(feedToRepository(result.current).map(item => item.id)).toEqual([
+      'user-1',
+      'assistant-stream-1',
+      'user-2'
+    ])
+  })
+})
diff --git a/apps/desktop/src/app/chat/runtime-repository.ts b/apps/desktop/src/app/chat/runtime-repository.ts
index 3dad84dac13..39b4d0c1d18 100644
--- a/apps/desktop/src/app/chat/runtime-repository.ts
+++ b/apps/desktop/src/app/chat/runtime-repository.ts
@@ -30,10 +30,22 @@ export function useRuntimeMessageRepository(messages: ChatMessage[]): ExportedMe
   return useMemo(() => {
     const items: { message: ThreadMessage; parentId: string | null }[] = []
     const branchParentByGroup = new Map<string, string | null>()
+    const seenIds = new Set<string>()
     let visibleParentId: string | null = null
     let headId: string | null = null
 
     for (const message of coalesceToolOnlyAssistants(messages, toolMergeCacheRef.current)) {
+      // A repeated id is a transcript bug upstream, but it must not reach the
+      // repository: MessageRepository throws on the second link ("A message
+      // with the same id already exists in the parent tree") and takes the
+      // whole workspace pane down with it. Keep the first occurrence — the
+      // later copy carries the same id, so it is the row we already rendered.
+      if (seenIds.has(message.id)) {
+        continue
+      }
+
+      seenIds.add(message.id)
+
       let parentId = visibleParentId
 
       if (message.role === 'assistant' && message.branchGroupId) {
diff --git a/apps/desktop/src/lib/inflight-turn-journal.ts b/apps/desktop/src/lib/inflight-turn-journal.ts
index e93a0f09754..2e4d0cb42f1 100644
--- a/apps/desktop/src/lib/inflight-turn-journal.ts
+++ b/apps/desktop/src/lib/inflight-turn-journal.ts
@@ -291,6 +291,16 @@ function overlayProjectionRow(projection: ChatMessage, journalRow: ChatMessage):
   return { ...merged, parts }
 }
 
+/** Rows the base transcript doesn't already hold by id. The journal and the
+ *  base can both carry the same row (a resume that replays a still-journaled
+ *  turn), and appending it twice puts a duplicate id in the transcript —
+ *  which assistant-ui's MessageRepository rejects by throwing. */
+function withoutBaseIds(rows: ChatMessage[], baseMessages: ChatMessage[]): ChatMessage[] {
+  const baseIds = new Set(baseMessages.map(message => message.id))
+
+  return rows.filter(row => !baseIds.has(row.id))
+}
+
 export function mergeInFlightMessages(
   baseMessages: ChatMessage[],
   tailMessages: ChatMessage[],
@@ -321,7 +331,13 @@ export function mergeInFlightMessages(
     // append the whole tail.
     const streamId = lastJournalRow?.id ?? null
 
-    return { applied: true, caughtUp: false, messages: [...baseMessages, ...tail], streamId, turnStartedAt: null }
+    return {
+      applied: true,
+      caughtUp: false,
+      messages: [...baseMessages, ...withoutBaseIds(tail, baseMessages)],
+      streamId,
+      turnStartedAt: null
+    }
   }
 
   const afterUser = baseMessages.slice(matchingUserIndex + 1)
@@ -350,7 +366,7 @@ export function mergeInFlightMessages(
     return {
       applied: true,
       caughtUp: false,
-      messages: [...baseMessages, ...tailAssistants],
+      messages: [...baseMessages, ...withoutBaseIds(tailAssistants, baseMessages)],
       streamId,
       turnStartedAt: null
     }