Thanks Adam.
All sqlite.bak files are 1MB.
I sync the folders to a cloud backup and then to a smaller portable device.

Thanks Adam. There seem to be three options.

1) I have some recent backups of the Zotero directory, from 6 December when my old laptop backed up to the cloud (the SQLite files are 92.88MB on this version) and an earlier version from mid-November on an external drive. If I downloaded those files or synced them to my new laptop, I could restore a recent version, and then hopefully sync with the new data on the server. Would that work?

2) If I do a regular sync, could the empty Zotero library be synced to the server, deleting all my references?

3) The preferences menu mentions that resetting data from the server can cause difficulties. Is that also a high risk approach?

I don't use Dropbox, and have a number of backup strategies, but they do not seem sufficient at the moment!

Thanks for your help.

Thanks Adam. I will try option 1), and will modify my daily backup schedule so it includes a daily backup of my Zotero directory to an external drive instead of a cloud backup.

Thank you Adam. Finally, a simple sync from the server to Zotero Standalone restored my library. I have now created a dated backup of zotero.sqlite and the storage folders elsewhere on my hard drive, backing up to an external drive at this writing.

I will try to remove my Zotero data directory from the cloud sync, but I need advice from my cloud backup provider on how to do this. The Changelog from the backup software indicates that the 96.55MB versions of zotero.sqlite and zotero.sqlite.bak were both deleted this afternoon during a sync, so it does seem that the cloud backup/sync software caused the problem.

Thank you again for your help.

Did the message say that your database was corrupted? If so, check if there's a zotero.sqlite.damaged file in your Zotero data directory, and try running it through the DB Repair Tool. First make a backup of your entire data directory.

Most likely your database got corrupted, Zotero automatically made a backup of the damaged DB and reverted to a clean database, and then Zotero synced down what was on the server, but you hadn't successfully synced in a couple months. (The last upload I see from you was at the end of October.)

was there an sqlite.damaged file that you tried to repair or was that the regular .sqlite?

I am currently not using a Firefox profile (not signed in) but don't think I was before either because I cannot sign in with any of my email addresses.

not sure what you mean by that. Firefox profiles are local, you don't need to sign into them (signing into Firefox is only for syncing profiles between computers).

When you previously were using Zotero, was that on the same computer? Also with Standalone? Could the message have said something about sharing the data directory with Firefox?

yeah, if you don't have .sqlite.damaged then what Dan suggested likely wasn't the case.

Another possibility might be that you somehow started a new data profile. Could you check what it says in the Advanced Tab of the Zotero Preferences --> Files and Folders under "Data directory location?" Is default checked, or does it specifcy a custom location (which)?

There isn't really any way to just lose data, but it's hard to say exactly what happened without knowing what the error message was. But if you don't see any files within your current Zotero data directory older than the other day, it's likely that there's another data directory elsewhere on your computer, so you could try searching for zotero.sqlite:

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

It doesn't look like you've uploaded anything to the server in over two years, so you'd have to find the data locally.

I've done extensive troubleshooting that consisted of the following:
- checked the Event Viewer for any issues regarding Zotero to see the error message from failed application start on the evening of Dec 24, but I didn't find any references to that event in the Windows Event Log. After selecting "Quit Zotero" in the error message and finally starting Zotero Standalone that evening, it loaded an old database with 80 records (where there should be hundreds more).
- checked Zotero sync options -- they were enabled the whole time.
- there were no .crashed files in the Zotero directory, but there is a store.json.mozlz4 file in the /crashed directory; however, the Zotero extension for Firefox was not used for months and there is a possibility that an automatic Firefox update from a few weeks ago disabled the Zotero extension.
- there are no multiple zotero.sqlite files on my computer. The only .sqlite and .sqlite.bak were in the defined (default) data directory so the issue is not coming from fiddling with the wrong database.
- I did not use Zotero on any other devices except for this laptop, so we can also exclude the possibility that the library was overwritten from another device.
- the Zotero Standalone data folder was not set up to any 3rd party cloud backup such as Dropbox, GDrive, Box, etc. It was only expected to sync with Zotero's online database.
- I backed up all of Zotero Standalone's profile files and the database was made before recovery attempts. I tried to restore the zotero.sqlite database and the zotero.sqlite.bak file, after the crash, but it seems that both files are actually the same, synced from Zotero's server.
- I also used my friend's computer (Zotero MacOSX) to try to restore the .sqlite and .sqlite.bak databases from the date of crash -- without sync options enabled -- and it seems that the database corresponds to what I have on my laptop and what is on Zotero's server, leading to the conclusion that my laptop synced with the server and downloaded what was in the library while overwriting my local data.

Literally years of research just vanished after an unwanted sync push. So, it appears that uploading from Standalone to Zotero online works (so we can rule out that a firewall or antivirus rule might block it the upload), however, the question is, with the sync enabled the whole time, why the local copy didn't update all the changes to the server's online database in over two years?

What Rintze says would have been my next step too.

One other possibility that occurred to me: Any chance you have a 2nd Zotero account and you're logged in (and synce with) the wrong one? We do see this surprisingly often.

What you suspect as having happend is incredibly unlikely to be the case. Zotero sync doesn't just overwrite local data -- it only ever deletes items when either
a) you have explicitly deleted the items or
b) you explicitly use the reset options in the sync preferences.
Neither of these sounds like is the case here.


Also, for the worst case, don't you have a backup of your harddisk for prior to the 24th? That should make restoring pretty easy.