diff --git a/apps/desktop/electron/bootstrap-runner.test.ts b/apps/desktop/electron/bootstrap-runner.test.ts
index a61cec77f59..7ba50c85e74 100644
--- a/apps/desktop/electron/bootstrap-runner.test.ts
+++ b/apps/desktop/electron/bootstrap-runner.test.ts
@@ -4,7 +4,15 @@ import os from 'node:os'
 import path from 'node:path'
 import test from 'node:test'
 
-import { cachedScriptPath, installedAgentInstallScript, resolveInstallScript, runBootstrap } from './bootstrap-runner'
+import {
+  buildPinArgs,
+  buildPosixPinArgs,
+  cachedScriptPath,
+  hasExistingGitCheckout,
+  installedAgentInstallScript,
+  resolveInstallScript,
+  runBootstrap
+} from './bootstrap-runner'
 
 const SCRIPT_NAME = process.platform === 'win32' ? 'install.ps1' : 'install.sh'
 
@@ -54,6 +62,58 @@ test('installedAgentInstallScript resolves the installer in the agent checkout',
   }
 })
 
+test('existing checkout detection requires git metadata', () => {
+  const home = mkTmpHome()
+
+  try {
+    const activeRoot = path.join(home, 'hermes-agent')
+    assert.equal(hasExistingGitCheckout(activeRoot), false)
+
+    fs.mkdirSync(path.join(activeRoot, '.git'), { recursive: true })
+    assert.equal(hasExistingGitCheckout(activeRoot), true)
+  } finally {
+    fs.rmSync(home, { recursive: true, force: true })
+  }
+})
+
+test('fresh bootstrap args include the packaged commit pin', () => {
+  const installStamp = { commit: 'a'.repeat(40), branch: 'main' }
+
+  assert.deepEqual(buildPinArgs(installStamp), ['-Commit', installStamp.commit, '-Branch', 'main'])
+  assert.deepEqual(
+    buildPosixPinArgs({
+      installStamp,
+      activeRoot: '/tmp/hermes-agent',
+      hermesHome: '/tmp/hermes'
+    }),
+    [
+      '--dir',
+      '/tmp/hermes-agent',
+      '--hermes-home',
+      '/tmp/hermes',
+      '--branch',
+      'main',
+      '--commit',
+      installStamp.commit
+    ]
+  )
+})
+
+test('existing-checkout bootstrap args keep branch but skip the packaged commit pin', () => {
+  const installStamp = { commit: 'a'.repeat(40), branch: 'main' }
+
+  assert.deepEqual(buildPinArgs(installStamp, { pinCommit: false }), ['-Branch', 'main'])
+  assert.deepEqual(
+    buildPosixPinArgs({
+      installStamp,
+      activeRoot: '/tmp/hermes-agent',
+      hermesHome: '/tmp/hermes',
+      pinCommit: false
+    }),
+    ['--dir', '/tmp/hermes-agent', '--hermes-home', '/tmp/hermes', '--branch', 'main']
+  )
+})
+
 test('resolveInstallScript prefers a cached script without touching the network', async () => {
   const home = mkTmpHome()
 
diff --git a/apps/desktop/electron/bootstrap-runner.ts b/apps/desktop/electron/bootstrap-runner.ts
index 21a8cb4cd5d..41ddd597a37 100644
--- a/apps/desktop/electron/bootstrap-runner.ts
+++ b/apps/desktop/electron/bootstrap-runner.ts
@@ -107,6 +107,18 @@ function installedAgentInstallScript(hermesHome) {
   }
 }
 
+function hasExistingGitCheckout(activeRoot) {
+  if (!activeRoot) {
+    return false
+  }
+
+  try {
+    return fs.existsSync(path.join(activeRoot, '.git'))
+  } catch {
+    return false
+  }
+}
+
 function cachedScriptPath(hermesHome, commit) {
   return path.join(bootstrapCacheDir(hermesHome), `install-${commit}.${process.platform === 'win32' ? 'ps1' : 'sh'}`)
 }
@@ -529,13 +541,14 @@ function spawnBash(scriptPath, args, { emit, stageName, abortSignal, hermesHome
 // Manifest + stage dispatch
 // ---------------------------------------------------------------------------
 
-// Build the install.ps1 pin args (-Commit / -Branch) from the install-stamp
-// so the repository stage clones the exact SHA the .exe was tested with
-// instead of falling back to install.ps1's default ($Branch = "main").
-function buildPinArgs(installStamp) {
+// Build the installer branch/pin args from the install stamp. The commit pin
+// is fresh-install only: once a managed checkout already exists, bootstrap is
+// a repair/update path and must not let an old packaged app detach the checkout
+// back to the commit baked into that app.
+function buildPinArgs(installStamp, { pinCommit = true } = {}) {
   const args = []
 
-  if (installStamp && installStamp.commit) {
+  if (pinCommit && installStamp && installStamp.commit) {
     args.push('-Commit', installStamp.commit)
   }
 
@@ -546,26 +559,34 @@ function buildPinArgs(installStamp) {
   return args
 }
 
-function buildPosixPinArgs({ installStamp, activeRoot, hermesHome }) {
+function buildPosixPinArgs({ installStamp, activeRoot, hermesHome, pinCommit = true }) {
   const args = ['--dir', activeRoot, '--hermes-home', hermesHome]
 
   if (installStamp && installStamp.branch) {
     args.push('--branch', installStamp.branch)
   }
 
-  if (installStamp && installStamp.commit) {
+  if (pinCommit && installStamp && installStamp.commit) {
     args.push('--commit', installStamp.commit)
   }
 
   return args
 }
 
-async function fetchManifest({ scriptPath, installerKind, emit, hermesHome, activeRoot, installStamp }) {
+async function fetchManifest({
+  scriptPath,
+  installerKind,
+  emit,
+  hermesHome,
+  activeRoot,
+  installStamp,
+  pinCommit
+}) {
   const isPosix = installerKind === 'posix'
 
   const args = isPosix
-    ? ['--manifest', ...buildPosixPinArgs({ installStamp, activeRoot, hermesHome })]
-    : ['-Manifest', ...buildPinArgs(installStamp)]
+    ? ['--manifest', ...buildPosixPinArgs({ installStamp, activeRoot, hermesHome, pinCommit })]
+    : ['-Manifest', ...buildPinArgs(installStamp, { pinCommit })]
 
   const result = await (isPosix ? spawnBash : spawnPowerShell)(scriptPath, args, {
     emit,
@@ -622,7 +643,17 @@ function parseStageResult(stdout) {
   return null
 }
 
-async function runStage({ scriptPath, installerKind, stage, emit, hermesHome, activeRoot, abortSignal, installStamp }) {
+async function runStage({
+  scriptPath,
+  installerKind,
+  stage,
+  emit,
+  hermesHome,
+  activeRoot,
+  abortSignal,
+  installStamp,
+  pinCommit
+}) {
   const startedAt = Date.now()
   emit({ type: 'stage', name: stage.name, state: 'running' })
 
@@ -634,9 +665,9 @@ async function runStage({ scriptPath, installerKind, stage, emit, hermesHome, ac
         stage.name,
         '--non-interactive',
         '--json',
-        ...buildPosixPinArgs({ installStamp, activeRoot, hermesHome })
+        ...buildPosixPinArgs({ installStamp, activeRoot, hermesHome, pinCommit })
       ]
-    : ['-Stage', stage.name, '-NonInteractive', '-Json', ...buildPinArgs(installStamp)]
+    : ['-Stage', stage.name, '-NonInteractive', '-Json', ...buildPinArgs(installStamp, { pinCommit })]
 
   const result = await (isPosix ? spawnBash : spawnPowerShell)(scriptPath, args, {
     emit,
@@ -774,6 +805,18 @@ async function runBootstrap(opts) {
   })
 
   try {
+    const existingCheckout = hasExistingGitCheckout(activeRoot)
+    const pinCommit = !existingCheckout
+
+    if (existingCheckout && installStamp && installStamp.commit) {
+      emit({
+        type: 'log',
+        line:
+          `[bootstrap] existing checkout detected at ${activeRoot}; ` +
+          `not pinning to packaged install stamp ${installStamp.commit.slice(0, 12)}`
+      })
+    }
+
     // 1. Resolve the platform installer.
     const scriptInfo = await resolveInstallScript({ installStamp, sourceRepoRoot, hermesHome, emit })
     const installerKind = scriptInfo.kind || 'powershell'
@@ -785,7 +828,8 @@ async function runBootstrap(opts) {
       emit,
       hermesHome,
       activeRoot,
-      installStamp
+      installStamp,
+      pinCommit
     })
 
     emit({
@@ -813,7 +857,8 @@ async function runBootstrap(opts) {
         hermesHome,
         activeRoot,
         abortSignal,
-        installStamp
+        installStamp,
+        pinCommit
       })
 
       if (ev.state === 'failed') {
@@ -847,7 +892,10 @@ async function runBootstrap(opts) {
 }
 
 export {
+  buildPinArgs,
+  buildPosixPinArgs,
   cachedScriptPath,
+  hasExistingGitCheckout,
   installedAgentInstallScript,
   // Exposed for testability
   parseStageResult,