diff --git a/src/main/ipc/runtime-environments/runtime-environment-session-reconcile.test.ts b/src/main/ipc/runtime-environments/runtime-environment-session-reconcile.test.ts
index 6e648ef84fb..d0ed0ed9365 100644
--- a/src/main/ipc/runtime-environments/runtime-environment-session-reconcile.test.ts
+++ b/src/main/ipc/runtime-environments/runtime-environment-session-reconcile.test.ts
@@ -1,13 +1,33 @@
 import { mkdtempSync, writeFileSync } from 'node:fs'
+import * as fs from 'node:fs'
 import { tmpdir } from 'node:os'
 import { join } from 'node:path'
-import { describe, expect, it, vi } from 'vitest'
+import { afterEach, describe, expect, it, vi } from 'vitest'
 import type { ExecutionHostId } from '../../../shared/execution-host'
 import { addEnvironmentFromPairingCode } from '../../../shared/runtime-environment-store'
 import { getEnvironmentStorePath } from '../../../shared/runtime-environment-store-file'
+import { getRuntimeEnvironmentSidecarPath } from '../../../shared/runtime-environment-sidecar'
 import { pairingCode } from './runtime-environments-ipc-test-harness'
 import { reconcileOrphanedRuntimeSessions } from './runtime-environment-session-reconcile'
 
+// Lets a test make the registry vanish between a presence check and its read.
+const fsRace = vi.hoisted(() => {
+  const existsAnswers: boolean[] = []
+  return { existsAnswers }
+})
+vi.mock('node:fs', async (importOriginal) => {
+  const actual = await importOriginal<typeof fs>()
+  return {
+    ...actual,
+    existsSync: (path: fs.PathLike) => fsRace.existsAnswers.shift() ?? actual.existsSync(path)
+  }
+})
+
+afterEach(() => {
+  fsRace.existsAnswers.length = 0
+  vi.restoreAllMocks()
+})
+
 function sessionStore(hostIds: ExecutionHostId[]) {
   return {
     getWorkspaceSessionHostIds: () => hostIds,
@@ -44,4 +64,41 @@ describe('reconciling orphaned runtime sessions at startup', () => {
     expect(reconcileOrphanedRuntimeSessions(store, corrupt)).toEqual([])
     expect(store.removeWorkspaceSessionHost).not.toHaveBeenCalled()
   })
+
+  it('keeps sessions of saved servers this build cannot read or currently hides', () => {
+    const userDataPath = mkdtempSync(join(tmpdir(), 'orca-session-reconcile-hidden-'))
+    const linked = addEnvironmentFromPairingCode(userDataPath, {
+      name: 'linked',
+      pairingCode: pairingCode()
+    })
+    const path = getEnvironmentStorePath(userDataPath)
+    const saved = JSON.parse(fs.readFileSync(path, 'utf8'))
+    saved.environments.push({ id: 'env-newer-format', kind: 'future-server' })
+    writeFileSync(path, JSON.stringify(saved), { mode: 0o600 })
+    // An entry this build cannot parse hides its server from listings.
+    writeFileSync(
+      getRuntimeEnvironmentSidecarPath(userDataPath),
+      JSON.stringify({ version: 1, entries: { [linked.id]: { futureLinkField: true } } }),
+      { mode: 0o600 }
+    )
+    vi.spyOn(console, 'warn').mockImplementation(() => undefined)
+    const store = sessionStore([
+      `runtime:${linked.id}`,
+      'runtime:env-newer-format',
+      'runtime:removed-env'
+    ])
+
+    expect(reconcileOrphanedRuntimeSessions(store, userDataPath)).toEqual(['runtime:removed-env'])
+    expect(store.removeWorkspaceSessionHost).toHaveBeenCalledTimes(1)
+  })
+
+  it('deletes nothing when the registry disappears between its presence check and read', () => {
+    const userDataPath = mkdtempSync(join(tmpdir(), 'orca-session-reconcile-race-'))
+    const store = sessionStore(['runtime:env-1'])
+    // Present when first checked, gone by the time the read looks again.
+    fsRace.existsAnswers.push(true, false)
+
+    expect(reconcileOrphanedRuntimeSessions(store, userDataPath)).toEqual([])
+    expect(store.removeWorkspaceSessionHost).not.toHaveBeenCalled()
+  })
 })
diff --git a/src/main/ipc/runtime-environments/runtime-environment-session-reconcile.ts b/src/main/ipc/runtime-environments/runtime-environment-session-reconcile.ts
index 17c1805e7c5..4af13ec073c 100644
--- a/src/main/ipc/runtime-environments/runtime-environment-session-reconcile.ts
+++ b/src/main/ipc/runtime-environments/runtime-environment-session-reconcile.ts
@@ -1,8 +1,6 @@
 /** Crashes and older unlink flows can leave runtime session partitions that listings advertise as orphaned hosts. */
-import { existsSync } from 'node:fs'
 import { parseExecutionHostId, type ExecutionHostId } from '../../../shared/execution-host'
-import { listEnvironments } from '../../../shared/runtime-environment-store'
-import { getEnvironmentStorePath } from '../../../shared/runtime-environment-store-file'
+import { readEnvironmentStoreRecords } from '../../../shared/runtime-environment-store-records'
 
 type SessionHostStore = {
   getWorkspaceSessionHostIds: () => ExecutionHostId[]
@@ -14,15 +12,19 @@ export function reconcileOrphanedRuntimeSessions(
   store: SessionHostStore,
   userDataPath: string
 ): ExecutionHostId[] {
-  // Missing or unreadable registry data cannot prove a server was removed.
-  if (!existsSync(getEnvironmentStorePath(userDataPath))) {
-    return []
-  }
   let known: Set<string>
   try {
-    known = new Set(listEnvironments(userDataPath).map((environment) => environment.id))
-  } catch (error) {
-    console.warn('[runtime-environments] skipped orphaned session reconcile:', error)
+    // Raw records, not the listing: newer-format and overlay-hidden servers are still saved.
+    const records = readEnvironmentStoreRecords(userDataPath, { requireStoreFile: true })
+    if (records.unreadable.some((record) => record.id === undefined)) {
+      return []
+    }
+    known = new Set([
+      ...records.environments.map((environment) => environment.id),
+      ...records.unreadable.map((record) => record.id ?? '')
+    ])
+  } catch {
+    // Missing or unreadable registry data cannot prove a server was removed.
     return []
   }
   // Runtime sessions are written only after their server is registered.
diff --git a/src/main/ipc/runtime-environments/runtime-environments.ts b/src/main/ipc/runtime-environments/runtime-environments.ts
index 118ab3ab940..f29570e3cd4 100644
--- a/src/main/ipc/runtime-environments/runtime-environments.ts
+++ b/src/main/ipc/runtime-environments/runtime-environments.ts
@@ -119,7 +119,11 @@ export function registerRuntimeEnvironmentHandlers(store: Store): void {
   stopPreferenceWatch?.()
   stopPreferenceWatch = watchRuntimeEnvironmentPreference(store, getUserDataPath(), () => {
     // CLI and recipe removals skip the Settings path; drop their session partitions here too.
-    reconcileOrphanedRuntimeSessions(store, getUserDataPath())
+    try {
+      reconcileOrphanedRuntimeSessions(store, getUserDataPath())
+    } catch (error) {
+      console.warn('[runtime-environments] orphaned session reconcile failed:', error)
+    }
     publishRuntimeEnvironmentCatalogChanged()
   })
   for (const pending of pendingSubscriptions.values()) {