diff --git a/src/main/ai-vault-search/session-search-deleted-sources.test.ts b/src/main/ai-vault-search/session-search-deleted-sources.test.ts
index 536320203b1..9602462becc 100644
--- a/src/main/ai-vault-search/session-search-deleted-sources.test.ts
+++ b/src/main/ai-vault-search/session-search-deleted-sources.test.ts
@@ -1,6 +1,5 @@
-import { mkdirSync } from 'node:fs'
 import { chmod, mkdir, rm, writeFile } from 'node:fs/promises'
-import { dirname, join } from 'node:path'
+import { join } from 'node:path'
 import { afterEach, beforeEach, expect, it } from 'vitest'
 import { resetTranscriptConsumersForTests } from '../ai-vault/session-transcript-consumers'
 import { retireDeletedSessionSearchSources } from './session-search-deleted-sources'
@@ -19,7 +18,6 @@ let removed: string[]
 beforeEach(async () => {
   resetTranscriptConsumersForTests()
   harness = await openSessionSearchIndexerHarness('ss-deleted-sources')
-  mkdirSync(dirname(harness.databasePath), { recursive: true })
   removed = []
   store = new SessionSearchStore(harness.databasePath)
   // Only the removal matters here; the store's own removal path has its own tests.
diff --git a/src/main/ai-vault-search/session-search-index-pass.test.ts b/src/main/ai-vault-search/session-search-index-pass.test.ts
index a9bd4ab7015..90b0aa545f8 100644
--- a/src/main/ai-vault-search/session-search-index-pass.test.ts
+++ b/src/main/ai-vault-search/session-search-index-pass.test.ts
@@ -1,6 +1,5 @@
-import { mkdirSync } from 'node:fs'
 import { appendFile, rm } from 'node:fs/promises'
-import { dirname, join } from 'node:path'
+import { join } from 'node:path'
 import { afterEach, beforeEach, expect, it } from 'vitest'
 import { resetSessionParseCacheForTests } from '../ai-vault/session-scanner-parse-cache'
 import { resetTranscriptConsumersForTests } from '../ai-vault/session-transcript-consumers'
@@ -44,7 +43,6 @@ function transcript(sessionId: string): string {
 }
 
 function openStore(): SessionSearchStore {
-  mkdirSync(dirname(harness.databasePath), { recursive: true })
   const opened = new SessionSearchStore(harness.databasePath, (error) => errors.push(error))
   registerSessionSearchIndexConsumer(opened)
   return opened
diff --git a/src/main/ai-vault-search/session-search-index-pass.ts b/src/main/ai-vault-search/session-search-index-pass.ts
index 10a8f382893..662a2ee3327 100644
--- a/src/main/ai-vault-search/session-search-index-pass.ts
+++ b/src/main/ai-vault-search/session-search-index-pass.ts
@@ -2,11 +2,11 @@ import { throwIfAiVaultScanCancelled } from '../ai-vault/ai-vault-scan-cancellat
 import { parserPublishesMessages } from '../ai-vault/session-scanner-agent-parser'
 import {
   createSessionParseStats,
-  invalidateSessionParseCacheEntry,
   parseAgentSessionFileCached,
   sessionParseCacheCoversTranscript,
   type SessionParseStats
 } from '../ai-vault/session-scanner-parse-cache'
+import { requestWholeTranscriptRead } from '../ai-vault/session-transcript-reader'
 import type { SessionFileCandidate } from '../ai-vault/session-scanner-types'
 import { fileIdentity, isSessionSearchFileCurrent } from './session-search-file-cursor'
 import type { SessionSearchCycleAllowance } from './session-search-reconcile-budget'
@@ -63,13 +63,20 @@ export async function runSessionSearchIndexPass(
       deferred.push(...candidates.slice(index))
       break
     }
-    // Two reasons to drop the session list's cursor, both of which end with
-    // the reader opening the file: the index has to re-read it whole, or the
-    // list is already done with it and would otherwise read nothing at all.
-    // The second is not an edge case: any file the list scanned before the
-    // index existed is in exactly that state.
+    // Two reasons to ask the reader for a whole read, both ending with the file
+    // actually being opened. `forced` covers a path the store handed back from
+    // `takeStale` or a caller invalidated: the reader would otherwise pick
+    // `append` from the session list's resume point and the consumer would
+    // decline it again, every cycle, forever.
+    //
+    // The second is the case no decline can reach. When the list's cursor
+    // already sits at this file's current stat, the parse reuses its cached fold
+    // and opens nothing at all, so no consumer is ever asked and there is
+    // nothing to record as stale. Every transcript the list scanned before the
+    // index existed is in that state, which is what first enablement inside a
+    // running app looks like.
     if (forced || sessionParseCacheCoversTranscript(candidate, process.platform)) {
-      invalidateSessionParseCacheEntry(candidate.file.path)
+      requestWholeTranscriptRead(candidate.file.path)
     }
     try {
       await parseAgentSessionFileCached(candidate, process.platform, stats)
diff --git a/src/main/ai-vault-search/session-search-indexer.test.ts b/src/main/ai-vault-search/session-search-indexer.test.ts
index 710da12e33d..f13a9ce3d09 100644
--- a/src/main/ai-vault-search/session-search-indexer.test.ts
+++ b/src/main/ai-vault-search/session-search-indexer.test.ts
@@ -212,7 +212,7 @@ it('restarts the backfill when the history window widens and purges when it narr
   expect(sessionsMatching('recent')).toEqual([SESSION_ID])
 })
 
-it('refuses writes while paused and bounds the queue it keeps', async () => {
+it('refuses writes while paused, remembers what it declined, and bounds both queues', async () => {
   const path = transcriptPath()
   await writeClaudeTranscript(path, ['indexed before the pause'], SESSION_ID)
   await newIndexer({ pendingLimit: 3 }).start()
@@ -225,14 +225,19 @@ it('refuses writes while paused and bounds the queue it keeps', async () => {
   await parseTranscript(path)
   await nextCycle()
   expect(sessionsMatching('paused')).toEqual([])
+  // A pause is the window in which reads are declined, so forgetting them would
+  // lose exactly the files the pause covered.
+  expect(indexer?.status().filesPending).toBe(1)
 
+  // A caller can keep invalidating right through the pause; that queue is capped.
   indexer?.invalidate(['/a', '/b', '/c', '/d', '/e'])
   const paused = indexer?.status()
-  expect(paused?.filesPending).toBe(3)
+  expect(paused?.filesPending).toBe(4)
   expect(paused?.droppedPending).toBe(2)
 
   await indexer?.resume()
   expect(sessionsMatching('paused')).toEqual([SESSION_ID])
+  expect(indexer?.status()).toMatchObject({ filesPending: 0, droppedPending: 2 })
   expect(indexer?.status().phase).not.toBe('paused')
 })
 
@@ -279,14 +284,29 @@ it('spends a cycle budget and rolls the rest into the next cycle', async () => {
   expect(sessionsMatching('budgeted')).toHaveLength(4)
 })
 
-it('indexes a transcript the session list had already parsed before it existed', async () => {
+// First enablement inside a running app is the normal case, not an edge: the
+// session list has been scanning since launch, so every transcript already has
+// a cursor sitting at its current stat and the index has nothing at all.
+it('fills an empty index over a warm session-list cache on the first reconcile', async () => {
+  const path = transcriptPath()
+  await writeClaudeTranscript(path, ['scanned before the index existed'], SESSION_ID)
+  // An ordinary parse now reuses its cached fold and opens no file, so no
+  // consumer is asked and there is nothing for a decline to record.
+  await parseTranscript(path)
+
+  newIndexer()
+  await indexer?.reconcile()
+
+  expect(sessionsMatching('scanned')).toEqual([SESSION_ID])
+})
+
+it('fills an empty index over a warm session-list cache on the first sweep', async () => {
   const path = transcriptPath()
   await writeClaudeTranscript(path, ['scanned before the index existed'], SESSION_ID)
-  // The list's cursor now sits at this file's current stat, so an ordinary
-  // parse reads nothing and the index would stay empty forever.
   await parseTranscript(path)
 
   await newIndexer().start()
+
   expect(sessionsMatching('scanned')).toEqual([SESSION_ID])
 })
 
diff --git a/src/main/ai-vault-search/session-search-indexer.ts b/src/main/ai-vault-search/session-search-indexer.ts
index 1a904c18487..db119e55124 100644
--- a/src/main/ai-vault-search/session-search-indexer.ts
+++ b/src/main/ai-vault-search/session-search-indexer.ts
@@ -1,5 +1,3 @@
-import { mkdirSync } from 'node:fs'
-import { dirname } from 'node:path'
 import { runSessionSearchBackfill } from './session-search-backfill'
 import { pauseBackfill } from './session-search-backfill-pacing'
 import {
@@ -329,14 +327,16 @@ export class SessionSearchIndexer {
   }
 
   private publishPending(): void {
+    // Both queues, because a caller cannot act on one of them: the store's
+    // re-read set and this indexer's roll-over queue are each bounded, and
+    // either overrunning means the same thing for coverage.
     this.indexingStatus.setPending(
       this.pending.size + (this.store?.pendingFileCount ?? 0),
-      this.pending.droppedCount
+      this.pending.droppedCount + (this.store?.droppedPendingFileCount ?? 0)
     )
   }
 
   private openStore(): void {
-    mkdirSync(dirname(this.options.databasePath), { recursive: true })
     const store = new SessionSearchStore(this.options.databasePath, this.onError)
     store.setRetentionCutoffMs(this.cutoffMs())
     store.setAcceptingWrites(!this.paused)
diff --git a/src/main/ai-vault-search/session-search-indexing-status.ts b/src/main/ai-vault-search/session-search-indexing-status.ts
index d0d51b5bf4b..0b1d6141775 100644
--- a/src/main/ai-vault-search/session-search-indexing-status.ts
+++ b/src/main/ai-vault-search/session-search-indexing-status.ts
@@ -17,7 +17,11 @@ export type SessionSearchIndexStatus = {
   bytesIndexed: number
   /** Queued re-reads: the store's stale set plus whatever the budget rolled over. */
   filesPending: number
-  /** Pending entries dropped at the bound, so a long pause cannot grow memory. */
+  /**
+   * Re-reads dropped at a bound, the indexer's queue and the store's re-read set
+   * together. Non-zero means the queue is knowingly incomplete, so coverage
+   * cannot be reported as whole until the next full sweep.
+   */
   droppedPending: number
   /** Unfinished writes the open tombstoned; a non-zero value means a crash. */
   recoveredRows: number