Files still in storage, but folders and organization seem to be outdated

erm2700
2020 M1 Mac, Mac OS Sequoia 15.6, Zotero is up to date.

At some point today, Zotero stopped responding (I could, inside a given folder, expand parent items to see what was inside them but not open any files). I force quit, and when I tried to re-open, it gave me a gray screen with nothing on it. I uninstalled and reinstalled Zotero and it reopened with a navigation lefthand sidebar that appears to reflect the organization of my files as it looked several months ago. When I navigate to my data directory manually and inspect the `storage` folder, I can search for and find PDFs that I added last week. If I search inside of Zotero for those files, nothing appears.

When I open the developer console, there are some warnings but no errors. When I run "Check Database Integrity" it says "Passed" and "No errors were found in the database.".

I have a .bak file from two days ago, but I'm not sure how I could use that to fix this issue, and I'm also not entirely sure what the issue is. I would love any and all advice anyone could give me about which files might be the problem.
  • erm2700
    edited 7 days ago
    Update: I was able to restore the zotero.sqlite and zotero.sqlite-journal files from yesterday, which show the up-to-date lefthand navigation sidebar, and all of my files, but I once again cannot open any of them in the Zotero UI. It hangs for several minutes and then opens a tab/window for it, but the screen is just gray, there is no PDF visible.

    I can, however, click "Show in Finder" and it hangs for several minutes but then does in fact show it in Finder, and I can open the PDF with Preview.

    So far in debugging: the test file exists on my hard drive, Zotero's data directory is pointing to it, and my file organization is back (still not sure which file within my data directory that is stored in, is it zotero.sqlite?). But something is wrong with whatever part of Zotero actually opens files, maybe?
  • dstillman
    It sounds like your database was corrupted. Are you using the default location for the Zotero data directory or a custom location?

    What do you mean when you say that you can't open files?
  • erm2700
    Sorry, I just edited the above comment with more information! It is a custom location. I have confirmed that Zotero is pointing to the custom locaation. Other relevant information may be that the custom location is synced with iCloud.
  • dstillman
    https://www.zotero.org/support/kb/data_directory_in_cloud_storage_folder
  • erm2700
    Well, that's helpful, but once I move it out of iCloud syncing, what might I try to do to restore the ability to open files?
  • dstillman
    edited 7 days ago
    We can't help until you do that. The problem may just go away. If it doesn't, we'd want to see a Debug ID from Zotero startup (using "Restart with Logging Enabled…") for reproducing it.
  • erm2700
    Update! I had to do a lot of manual copying, re-downloading, and copying of file names so that the sqlite database would match the files in the storage folder (iCloud makes it extremely difficult to extract folders if they've synced and "unloaded" from your physical harddrive- it's as if Apple puts them in the coldest storage possible) but now it's working again.

    Whatever this was, it was an iCloud issue.
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