Upgrade StorageRecent RIS imports and downloaded PDFs missing after closing and reopening Zotero
Hello Zotero team,
I need help investigating apparent local data loss and preventing it from happening again. Recovering or reimporting the missing references is secondary to identifying the cause.
What happened
- I had kept Zotero running for a long time. During roughly the last 7-8 hours of that session, I imported batches of references from RIS files and used the Sci-Hub plugin to download PDFs.
- Before closing Zotero, I personally saw the imported items in the intended collections in the Zotero desktop window and could double-click and open their PDFs. This was not merely a browser save notification.
- After closing and reopening Zotero, the recent items were missing. Three collections were empty, and a fourth retained only seven items, although I had imported more.
- I did not see an update, database upgrade, repair, or backup-restore prompt when reopening.
- The sync tooltip said that the last sync was approximately 7-8 hours earlier. I subsequently disabled automatic syncing while investigating. I understand that local saving should not depend on successful syncing.
Affected collections and examples
- 1962, volume 21, issue 2 (April), issue 3 (July), and issue 4 (October): collections remain but the items are missing.
- 1962, volume 21, issue 1 (January): only seven items titled "Review of" remain.
- Missing examples: "The Loves of Pancho Villa" and "Folkways of the Mormons from the Journals of John D. Lee".
- A preceding batch is still present: "The Caesarean Delivery of Paul Bunyan", in 1963, volume 22, issue 1, has both its bibliographic item and its local PDF.
Environment
- Windows 11. The local upgrade.log reports Zotero 10.0.5 (x64), Windows 11 build 26200, and zh-CN locale.
- Custom data directory: D:\Zotero. This directory also contains zotero.exe and application installation files.
- Extensions listed in upgrade.log: Translate for Zotero 2.4.7; Better Notes for Zotero 3.3.3; Jasminum 1.1.39; Del Item With Attachment 0.5.0; Ethereal Reference 1.8.22; Sci-Hub Plugin for Zotero 2.0.0.
- These versions are from the log, not a fresh About-dialog report.
Checks already performed
An assistant used local tools to copy the databases and inspect the copies. The original databases were not edited, replaced, repaired, or restored by the assistant.
- A fresh database copy was preserved after Zotero had exited. At that point zotero.sqlite-wal was zero bytes.
- Neither missing example was found in the current database copy or either available automatic backup, including item records marked as deleted. The three affected collections had zero collection-item associations in all three database copies.
- Searches for "The Loves of Pancho Villa" in attachment filenames and existing extracted-text caches did not locate it. This was not an exhaustive PDF-content or disk-recovery search.
- SQLite PRAGMA quick_check returned "ok" on the current database copy. This is a structural check, not proof that all expected data is present.
- The latest deletedItems timestamp was September 30, and syncDeleteLog was empty in the inspected copy. We do not interpret this as conclusive proof that no deletion occurred.
Timeline (all times below converted to China Standard Time, UTC+8)
- The retained "The Caesarean Delivery of Paul Bunyan" item was added October 1, 2026 at 18:01:56; its attachment was added at 18:02:01, and the PDF exists locally.
- The seven retained "Review of" items in the January 1962 collection all have dateAdded October 1 at 20:47:58.
- Two attachments under those seven items have dateAdded October 2 at 01:21:38 and 01:22:04.
- zotero.sqlite.bak had filesystem modification time October 2 at 01:16:44, but its latest item dateAdded was October 1 at 18:03:15.
- zotero.sqlite.1.bak had filesystem modification time October 1 at 12:19:29, and its latest item dateAdded was September 30 at 22:46:38.
- upgrade.log was modified October 2 at 01:16:44 and contains a schema migration from version 129 to 130. I did not see an upgrade prompt. We have not established that this migration caused the missing data.
The loss therefore does not appear to be a simple cutoff at the last successful sync: some later records survived while entire earlier imported batches are absent. The exact point at which the data disappeared is unknown; I noticed it after restarting.
Questions
1. How can items and PDFs that were visible and usable during a session be absent after reopening? What evidence would distinguish an uncommitted/rolled-back transaction, plugin interference, database replacement, or another cause?
2. Are there known issues relevant to this version, RIS import workflow, or installed extensions?
3. What specific diagnostic logs or controlled reproduction steps should I collect, preferably using a separate test library so I do not risk the remaining data?
4. Should the shared installation/data directory be changed, and what other concrete configuration changes are needed to prevent recurrence?
I also encountered anecdotal reports of similar symptoms on Xiaohongshu in China (recent items missing after restarting following a long-running session). I have not verified those reports and do not claim they share the same cause.
No Report ID or Debug ID has been collected yet, and no controlled reproduction has been performed. Please advise what information you need next. I can provide relevant screenshots or logs on request, with personal information removed.
I need help investigating apparent local data loss and preventing it from happening again. Recovering or reimporting the missing references is secondary to identifying the cause.
What happened
- I had kept Zotero running for a long time. During roughly the last 7-8 hours of that session, I imported batches of references from RIS files and used the Sci-Hub plugin to download PDFs.
- Before closing Zotero, I personally saw the imported items in the intended collections in the Zotero desktop window and could double-click and open their PDFs. This was not merely a browser save notification.
- After closing and reopening Zotero, the recent items were missing. Three collections were empty, and a fourth retained only seven items, although I had imported more.
- I did not see an update, database upgrade, repair, or backup-restore prompt when reopening.
- The sync tooltip said that the last sync was approximately 7-8 hours earlier. I subsequently disabled automatic syncing while investigating. I understand that local saving should not depend on successful syncing.
Affected collections and examples
- 1962, volume 21, issue 2 (April), issue 3 (July), and issue 4 (October): collections remain but the items are missing.
- 1962, volume 21, issue 1 (January): only seven items titled "Review of" remain.
- Missing examples: "The Loves of Pancho Villa" and "Folkways of the Mormons from the Journals of John D. Lee".
- A preceding batch is still present: "The Caesarean Delivery of Paul Bunyan", in 1963, volume 22, issue 1, has both its bibliographic item and its local PDF.
Environment
- Windows 11. The local upgrade.log reports Zotero 10.0.5 (x64), Windows 11 build 26200, and zh-CN locale.
- Custom data directory: D:\Zotero. This directory also contains zotero.exe and application installation files.
- Extensions listed in upgrade.log: Translate for Zotero 2.4.7; Better Notes for Zotero 3.3.3; Jasminum 1.1.39; Del Item With Attachment 0.5.0; Ethereal Reference 1.8.22; Sci-Hub Plugin for Zotero 2.0.0.
- These versions are from the log, not a fresh About-dialog report.
Checks already performed
An assistant used local tools to copy the databases and inspect the copies. The original databases were not edited, replaced, repaired, or restored by the assistant.
- A fresh database copy was preserved after Zotero had exited. At that point zotero.sqlite-wal was zero bytes.
- Neither missing example was found in the current database copy or either available automatic backup, including item records marked as deleted. The three affected collections had zero collection-item associations in all three database copies.
- Searches for "The Loves of Pancho Villa" in attachment filenames and existing extracted-text caches did not locate it. This was not an exhaustive PDF-content or disk-recovery search.
- SQLite PRAGMA quick_check returned "ok" on the current database copy. This is a structural check, not proof that all expected data is present.
- The latest deletedItems timestamp was September 30, and syncDeleteLog was empty in the inspected copy. We do not interpret this as conclusive proof that no deletion occurred.
Timeline (all times below converted to China Standard Time, UTC+8)
- The retained "The Caesarean Delivery of Paul Bunyan" item was added October 1, 2026 at 18:01:56; its attachment was added at 18:02:01, and the PDF exists locally.
- The seven retained "Review of" items in the January 1962 collection all have dateAdded October 1 at 20:47:58.
- Two attachments under those seven items have dateAdded October 2 at 01:21:38 and 01:22:04.
- zotero.sqlite.bak had filesystem modification time October 2 at 01:16:44, but its latest item dateAdded was October 1 at 18:03:15.
- zotero.sqlite.1.bak had filesystem modification time October 1 at 12:19:29, and its latest item dateAdded was September 30 at 22:46:38.
- upgrade.log was modified October 2 at 01:16:44 and contains a schema migration from version 129 to 130. I did not see an upgrade prompt. We have not established that this migration caused the missing data.
The loss therefore does not appear to be a simple cutoff at the last successful sync: some later records survived while entire earlier imported batches are absent. The exact point at which the data disappeared is unknown; I noticed it after restarting.
Questions
1. How can items and PDFs that were visible and usable during a session be absent after reopening? What evidence would distinguish an uncommitted/rolled-back transaction, plugin interference, database replacement, or another cause?
2. Are there known issues relevant to this version, RIS import workflow, or installed extensions?
3. What specific diagnostic logs or controlled reproduction steps should I collect, preferably using a separate test library so I do not risk the remaining data?
4. Should the shared installation/data directory be changed, and what other concrete configuration changes are needed to prevent recurrence?
I also encountered anecdotal reports of similar symptoms on Xiaohongshu in China (recent items missing after restarting following a long-running session). I have not verified those reports and do not claim they share the same cause.
No Report ID or Debug ID has been collected yet, and no controlled reproduction has been performed. Please advise what information you need next. I can provide relevant screenshots or logs on request, with personal information removed.