Loss of collections after Zotero update and sync (Windows 11)

carmencar

Hello everyone,

After updating Zotero to version 9.0.4 on Windows 11, all my collections (folders) suddenly disappeared. Everything has been merged into “My Library”.

All my items are still there and all attached PDFs are still present. Only the collection/folder structure is gone.

This structure included ~10 years of organization (multiple thematiccollections such as research projects, reading categories, etc.).

What I have already checked:
Local Zotero data directory: C:\Users\Username\Zotero
zotero.sqlite exists
zotero.sqlite.bak and zotero.sqlite.1.bak exist
Restoring these backups does not recover the missing collections (they already reflect the “flattened” state)
Zotero sync does not show any recovery or history options
Windows File History is disabled
OneDrive does not contain Zotero data
File recovery tools (Recuva) did not find older SQLite versions
No other zotero.sqlite files exist on the system
Problem description:

It seems that after the update/sync, the collection structure was overwritten and propagated both locally and to zotero.org.

Questions:
Is there any known issue in Zotero 9.x where collection structure can be lost or flattened after sync/update?
Is there any server-side backup or snapshot system for Zotero libraries that could allow recovery of previous collection structures?
Is there any additional recovery method (beyond local SQLite backups) that I might have missed?

Any help would be greatly appreciated.

Thank you.

dstillman

Nothing to do with an update — that doesn't affect data. All your collections were deleted in the online library on March 7, 2026 from a Zotero 7.0.32 installation on Windows. Only you would know what might have done that. (Sometimes this happens when people leave themselves logged in on some shared computer. If you think that's possible, you should clear all application sessions from your security settings.) Assuming this happened on another computer and you didn't sync between then and now, you'd only see the collections disappear now.

You'd have to find a backup from before that date, and then you could follow the steps here about restoring deleted collections:

https://www.zotero.org/support/zotero_data#restoring_your_zotero_data_from_a_backup_and_overwriting_synced_changes

carmencar

Thank you, that explains what happened. I had left Zotero logged in on a work computer, and that machine was reset around that time.

Unfortunately, I do not appear to have any local backup from before March 7, 2026. The available zotero.sqlite backups already reflect the post-deletion state (even though I have been using this computer with the same Zotero account for years).

Given these circumstances, is there any possibility that server-side snapshots, archives, logs, or any other recovery mechanism might exist for restoring the collection structure, or is recovery impossible without a pre-March 7 local backup?

Thank you again for your help.

dstillman

No, sorry, we wouldn't have any way of restoring those.