Problems with older versions of library structure in group library

We are a large group from different organizations, who are experiencing some problems with securing the corrections in our group library structure (names, former deletions etc.).

There is no problems with the bibliographic information (5200 in number), but again and again older deleted structures pop up again in spite of rigorous backup procedure
(one at a time, at a specific time, no automatic synchronization); seemingly overwriting later versions.

Is there any way where we can check what the library structure looks like directly from the zotero.sqlite, in order to avoid other more labourous procedures?

Thank you very much
Erik Schwägermann
  • My expectation would be that this will just work much better if you all switch to Zotero 5. Zotero 4 handles tags and collections during sync in a way that make conflicts hard to avoid in large groups (and then restores deleted tags and items from collections on syncing).

    (To your question directly, what you're seeing in Zotero is the structure in the sqlite. The problem are sync conflicts--the library structure is different in different places).
  • Thank you for a quick answer. I will have a go at it, using Zotero 5. I just thought that some of the sync problems could be reduced by taking a back up of the sqlite Erik Schwägermann
  • Also, we strongly recommend automatic sync--in general, but particularly for groups; contrary what you seem to suggest, it actually makes sync conflicts much less likely.
  • I am a member of the above mentioned group and I am still experiencing the problems despite being the only person who now has access to the group library. All other members have now been uninvited/removed from the group (except the account that was used to create the group which is not used by anyone).
    Automatic sync is on, and I'm using Zotero 5 with the new connector.

    I have been moving items and deleting unwanted collections for two days without any problems. Then, yesterday, the last two collections I deleted before syncing and closing Zotero returned the next time I opened Zotero. It’s like the last changes I made have been undone. One of the collections contained items that I had removed one at a time after copying them to other collections. These items are now only in the collection that I deleted and not in any of the collections I copied them to.

    I would like to make a Debug ID next time deleted items/collections reappear, but that is difficult since I don’t know when it will happen.

    Question 1:
    Maybe the following is a clue as to what is wrong: After the deleted collections returned, I tried deleting the other (empty) collection again, clicked on the sync button and went to the group library on The collection I had just deleted was still there, which I find surprising. It did, however, disappear after about 15-30 minutes. I am not sure whether this delay is normal or perhaps a clue as to what could be causing the problems?

    Question 2:
    What is the best way to restore my Library using my latest backup? I'm thinking that the (unwanted) changes that happened since the backup will be applied to my restored database when I sync.
    I've read "Restoring your Zotero library from a backup and overwriting synced changes" (, but this seems to be meant for situations where specific items or collections have been deleted. In this situation, however, many items are now missing from many different collections (and are back where they came from).
  • No, @danstillman will need to look at these. The scenario you describe should just not be possible with Zotero 5 (or 4, for that matter -- there, deletions from collections might be reverted but not additions).
  • Question 2 is the most urgent one. I would like to restore the library using my latest backup, but I'm wondering if the unwanted changes will be reapplied when I sync. In that case, is there some way I can overwrite the server data (I think that's the right term)?.

    @danstillman (or anyone)?
  • Yeah, what you describe shouldn't really be possible. If a deletion goes through to the server, that data (e.g., the collection name) is removed and can't be restored unless another client reuploads it, and as adamsmith says, that wouldn't result in the removal of new data, only the potential restoration of deleted data.

    So if changes — including additions — appear to have been rolled back (and assuming you're not misremembering), it seems more likely that 1) those changes never synced and 2) you somehow ended up on an earlier version of your database than the one you were using previously.
    I would like to restore the library using my latest backup, but I'm wondering if the unwanted changes will be reapplied when I sync.
    Have you checked to see if your backup actually has the data you think it has? If not, I would temporarily disable auto-sync, make two empty folders, copy your current zotero.sqlite into one and your backup zotero.sqlite into the other, and then point Zotero at each one from the Advanced → Files and Folders pane of the Zotero preferences and inspect the data in each. If you do see the data you expect in the backup, it'd be helpful if you could send screenshots of the data (or lack thereof) in your current DB, backup DB, and online library to with a link to this thread.
    is there some way I can overwrite the server data
    Not currently, but again, that doesn't really make sense here, because these wouldn't be server-side changes. So let's start with the above.
  • OK. I checked, and it turns out my backup is from before I made these last changes. Darn. But I'm sure did I move these items to other folders, then synced and closed Zotero. Also, moving them took long enough for Zotero to have synchronized automatically several times. Maybe, as you suggest, the changes never synced properly.. I don't know. Confusing.

    I'll just have to do the work again (luckily it’s not that much), and keep making backups often in case something like this should happen again.
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