diff --git a/packages/server/src/settings/service.test.ts b/packages/server/src/settings/service.test.ts
index 505a5cca..d169c090 100644
--- a/packages/server/src/settings/service.test.ts
+++ b/packages/server/src/settings/service.test.ts
@@ -28,7 +28,7 @@ describe("SettingsService config persistence", () => {
   it("normalizes and persists a server-owner patch once", () => {
     let writes = 0
     const service = serviceWithStore({
-      getOwner: () => ({ logLevel: "info", sidecars: [] }),
+      getOwner: () => ({ logLevel: "info", opencodeBinary: "opencode", sidecars: [] }),
       replaceOwner: (_owner: string, value: unknown) => {
         writes += 1
         return value
@@ -38,7 +38,7 @@ describe("SettingsService config persistence", () => {
 
     const result = service.mergePatchOwner("config", "server", { sidecars: [{ id: "one" }] })
     assert.equal(writes, 1)
-    assert.deepEqual(result, { logLevel: "INFO", sidecars: [{ id: "one" }] })
+    assert.deepEqual(result, { logLevel: "INFO", opencodeBinary: "opencode2", sidecars: [{ id: "one" }] })
   })
 
   it("does not report a persisted patch as failed when an event listener throws", () => {
diff --git a/packages/server/src/settings/service.ts b/packages/server/src/settings/service.ts
index 7bb10e72..4e52dd44 100644
--- a/packages/server/src/settings/service.ts
+++ b/packages/server/src/settings/service.ts
@@ -40,6 +40,9 @@ function normalizeServerConfigOwner(value: SettingsDoc): SettingsDoc {
   } else if (next.logLevel !== undefined) {
     next.logLevel = "DEBUG"
   }
+  if (next.opencodeBinary === "opencode") {
+    next.opencodeBinary = "opencode2"
+  }
   return next
 }
 
diff --git a/packages/ui/src/components/opencode-binary-selector.tsx b/packages/ui/src/components/opencode-binary-selector.tsx
index e5455016..92e3581d 100644
--- a/packages/ui/src/components/opencode-binary-selector.tsx
+++ b/packages/ui/src/components/opencode-binary-selector.tsx
@@ -30,7 +30,6 @@ const OpenCodeBinarySelector: Component<OpenCodeBinarySelectorProps> = (props) =
     addOpenCodeBinary,
     removeOpenCodeBinary,
     serverSettings,
-    updateLastUsedBinary,
   } = useConfig()
   const [customPath, setCustomPath] = createSignal("")
   const [validating, setValidating] = createSignal(false)
@@ -157,7 +156,6 @@ const OpenCodeBinarySelector: Component<OpenCodeBinarySelectorProps> = (props) =
     if (validation.valid) {
       addOpenCodeBinary(path, validation.version)
       props.onBinaryChange(path)
-      updateLastUsedBinary(path)
       setCustomPath("")
       setValidationError(null)
     } else {
@@ -182,7 +180,6 @@ const OpenCodeBinarySelector: Component<OpenCodeBinarySelectorProps> = (props) =
     if (props.disabled) return
     if (path === props.selectedBinary) return
     props.onBinaryChange(path)
-    updateLastUsedBinary(path)
   }
 
   function handleRemoveBinary(path: string, event: Event) {
@@ -192,7 +189,6 @@ const OpenCodeBinarySelector: Component<OpenCodeBinarySelectorProps> = (props) =
 
     if (props.selectedBinary === path) {
       props.onBinaryChange("opencode2")
-      updateLastUsedBinary("opencode2")
     }
   }
 
diff --git a/packages/ui/src/lib/hooks/use-app-session-capture.test.ts b/packages/ui/src/lib/hooks/use-app-session-capture.test.ts
index eaafcb59..7d4e9488 100644
--- a/packages/ui/src/lib/hooks/use-app-session-capture.test.ts
+++ b/packages/ui/src/lib/hooks/use-app-session-capture.test.ts
@@ -24,3 +24,7 @@ it("resumes capture only after native shutdown cancellation", () => {
   assert.match(capture, /listen<\{ generation: number \}>\("client-state:flush-cancelled"/)
   assert.match(capture, /if \(nativeShutdownGeneration !== payload\.generation\) return[\s\S]*nativeShutdownGeneration = null[\s\S]*schedule\(\)/)
 })
+
+it("waits for server storage writes during native shutdown", () => {
+  assert.match(capture, /nativeShutdown \? \[storage\.flushWrites\(\)\] : \[\]/)
+})
diff --git a/packages/ui/src/lib/hooks/use-app-session-capture.ts b/packages/ui/src/lib/hooks/use-app-session-capture.ts
index 7c7e5bd4..5c24d16d 100644
--- a/packages/ui/src/lib/hooks/use-app-session-capture.ts
+++ b/packages/ui/src/lib/hooks/use-app-session-capture.ts
@@ -7,6 +7,7 @@ import {
   clientStateIsPrimary, flushClientState, restorePreviousStateEnabled, updateRestorableSession,
   type RestorableSessionState, type RestorableTabState, type RestorableWorkspaceTabState,
 } from "../../stores/client-state"
+import { storage } from "../storage"
 import { normalizeWorkspacePath } from "../../stores/app-session-reconciliation"
 import {
   createRestorableSessionPreservation, createRestoredTabCommitGuard, markPreservedWorkspaceRemoved,
@@ -178,7 +179,10 @@ export function useAppSessionCapture() {
         : current
       updateRestorableSession(state)
     }
-    await flushClientState()
+    await Promise.all([
+      flushClientState(),
+      ...(nativeShutdown ? [storage.flushWrites()] : []),
+    ])
   }
   const nativeUnlisteners: Array<() => void> = []
   let nativeDisposed = false
diff --git a/packages/ui/src/lib/storage.test.ts b/packages/ui/src/lib/storage.test.ts
new file mode 100644
index 00000000..6ec387ee
--- /dev/null
+++ b/packages/ui/src/lib/storage.test.ts
@@ -0,0 +1,29 @@
+import assert from "node:assert/strict"
+import { afterEach, it } from "node:test"
+import { serverApi } from "./api-client"
+import { ServerStorage } from "./storage"
+
+const originalPatchConfigOwner = serverApi.patchConfigOwner
+
+afterEach(() => {
+  serverApi.patchConfigOwner = originalPatchConfigOwner
+})
+
+it("flushes an in-flight server write", async () => {
+  let resolveWrite!: (value: Record<string, unknown>) => void
+  serverApi.patchConfigOwner = <T extends Record<string, unknown>>() => new Promise<T>((resolve) => {
+    resolveWrite = (value) => resolve(value as T)
+  })
+  const storage = new ServerStorage()
+  const write = storage.patchConfigOwner("server", { opencodeBinary: "opencode2" })
+  let flushed = false
+  const flush = storage.flushWrites().then(() => {
+    flushed = true
+  })
+
+  await Promise.resolve()
+  assert.equal(flushed, false)
+  resolveWrite({ opencodeBinary: "opencode2" })
+  await flush
+  assert.deepEqual(await write, { opencodeBinary: "opencode2" })
+})
diff --git a/packages/ui/src/lib/storage.ts b/packages/ui/src/lib/storage.ts
index 4616bc94..ec4de3b8 100644
--- a/packages/ui/src/lib/storage.ts
+++ b/packages/ui/src/lib/storage.ts
@@ -39,6 +39,7 @@ export class ServerStorage {
   private instanceDataCache = new Map<string, InstanceData>()
   private instanceDataListeners = new Map<string, Set<(data: InstanceData) => void>>()
   private instanceLoadPromises = new Map<string, Promise<InstanceData>>()
+  private pendingWrites = new Set<Promise<unknown>>()
 
   constructor() {
     serverEvents.on("storage.configChanged", (event: WorkspaceEventPayload) => {
@@ -77,10 +78,11 @@ export class ServerStorage {
     return this.configOwnerLoadPromises.get(owner)!
   }
 
-  async patchConfigOwner(owner: string, patch: unknown): Promise<OwnerBucket> {
-    const updated = await serverApi.patchConfigOwner<OwnerBucket>(owner, patch)
-    this.setOwnerCache("config", owner, updated)
-    return updated
+  patchConfigOwner(owner: string, patch: unknown): Promise<OwnerBucket> {
+    return this.trackWrite(serverApi.patchConfigOwner<OwnerBucket>(owner, patch).then((updated) => {
+      this.setOwnerCache("config", owner, updated)
+      return updated
+    }))
   }
 
   async loadStateOwner(owner: string): Promise<OwnerBucket> {
@@ -103,10 +105,11 @@ export class ServerStorage {
     return this.stateOwnerLoadPromises.get(owner)!
   }
 
-  async patchStateOwner(owner: string, patch: unknown): Promise<OwnerBucket> {
-    const updated = await serverApi.patchStateOwner<OwnerBucket>(owner, patch)
-    this.setOwnerCache("state", owner, updated)
-    return updated
+  patchStateOwner(owner: string, patch: unknown): Promise<OwnerBucket> {
+    return this.trackWrite(serverApi.patchStateOwner<OwnerBucket>(owner, patch).then((updated) => {
+      this.setOwnerCache("state", owner, updated)
+      return updated
+    }))
   }
 
   async loadInstanceData(instanceId: string): Promise<InstanceData> {
@@ -133,15 +136,23 @@ export class ServerStorage {
     return this.instanceLoadPromises.get(instanceId)!
   }
 
-  async saveInstanceData(instanceId: string, data: InstanceData): Promise<void> {
+  saveInstanceData(instanceId: string, data: InstanceData): Promise<void> {
     const normalized = this.normalizeInstanceData(data)
-    await serverApi.writeInstanceData(instanceId, normalized)
-    this.setInstanceDataCache(instanceId, normalized)
+    return this.trackWrite(serverApi.writeInstanceData(instanceId, normalized).then(() => {
+      this.setInstanceDataCache(instanceId, normalized)
+    }))
   }
 
-  async deleteInstanceData(instanceId: string): Promise<void> {
-    await serverApi.deleteInstanceData(instanceId)
-    this.setInstanceDataCache(instanceId, DEFAULT_INSTANCE_DATA)
+  deleteInstanceData(instanceId: string): Promise<void> {
+    return this.trackWrite(serverApi.deleteInstanceData(instanceId).then(() => {
+      this.setInstanceDataCache(instanceId, DEFAULT_INSTANCE_DATA)
+    }))
+  }
+
+  async flushWrites(): Promise<void> {
+    while (this.pendingWrites.size > 0) {
+      await Promise.allSettled(this.pendingWrites)
+    }
   }
 
   onConfigOwnerChanged(owner: string, listener: (value: OwnerBucket) => void): () => void {
@@ -225,6 +236,12 @@ export class ServerStorage {
     }
   }
 
+  private trackWrite<T>(write: Promise<T>): Promise<T> {
+    this.pendingWrites.add(write)
+    void write.finally(() => this.pendingWrites.delete(write)).catch(() => undefined)
+    return write
+  }
+
   private normalizeInstanceData(data?: InstanceData | null): InstanceData {
     const source = data ?? DEFAULT_INSTANCE_DATA
     const messageHistory = Array.isArray(source.messageHistory) ? [...source.messageHistory] : []
diff --git a/packages/ui/src/stores/preferences.test.ts b/packages/ui/src/stores/preferences.test.ts
index 64dfddb8..5fc7aefa 100644
--- a/packages/ui/src/stores/preferences.test.ts
+++ b/packages/ui/src/stores/preferences.test.ts
@@ -1,7 +1,7 @@
 import assert from "node:assert/strict"
 import { describe, it } from "node:test"
 import { buildSpeechPatch } from "../lib/speech-patch"
-import { buildBinaryList, type SpeechSettingsUpdate } from "./preferences"
+import { buildBinaryList, normalizeServerConfig, type SpeechSettingsUpdate } from "./preferences"
 
 describe("buildBinaryList", () => {
   it("does not add built-in commands to custom binary history", () => {
@@ -13,6 +13,13 @@ describe("buildBinaryList", () => {
   })
 })
 
+describe("normalizeServerConfig", () => {
+  it("maps the legacy system command to opencode2", () => {
+    assert.equal(normalizeServerConfig({ opencodeBinary: "opencode" }).opencodeBinary, "opencode2")
+    assert.equal(normalizeServerConfig({ opencodeBinary: "C:/tools/opencode2.exe" }).opencodeBinary, "C:/tools/opencode2.exe")
+  })
+})
+
 describe("buildSpeechPatch", () => {
   it("only includes fields that are explicitly provided", () => {
     const patch = buildSpeechPatch({ ttsVoice: "alloy" })
diff --git a/packages/ui/src/stores/preferences.tsx b/packages/ui/src/stores/preferences.tsx
index 94222522..ebef51de 100644
--- a/packages/ui/src/stores/preferences.tsx
+++ b/packages/ui/src/stores/preferences.tsx
@@ -454,7 +454,7 @@ function normalizeUiState(input?: UiStateBucket | null): NormalizedUiState {
   }
 }
 
-function normalizeServerConfig(
+export function normalizeServerConfig(
   input?: ServerConfigBucket | null,
 ): Required<Pick<ServerConfigBucket, "listeningMode" | "logLevel" | "environmentVariables" | "opencodeBinary" | "secureEnvVars">> & { speech: SpeechSettings } {
   const source = input ?? {}
@@ -463,7 +463,9 @@ function normalizeServerConfig(
     source.logLevel === "INFO" || source.logLevel === "WARN" || source.logLevel === "ERROR" || source.logLevel === "DEBUG"
       ? source.logLevel
       : "DEBUG"
-  const opencodeBinary = typeof source.opencodeBinary === "string" && source.opencodeBinary.trim() ? source.opencodeBinary : "opencode2"
+  const opencodeBinary = typeof source.opencodeBinary === "string" && source.opencodeBinary.trim() && source.opencodeBinary !== "opencode"
+    ? source.opencodeBinary
+    : "opencode2"
   const environmentVariables = normalizeRecord(source.environmentVariables)
   const secureEnvVars = normalizeSecureEnvVars(source.secureEnvVars)
   const speech = normalizeSpeechSettings(source.speech)