Why did all my work get deleted?

I am just... I can't even explain how crushed I am.

I have spent a lot of time building my database. It turns out I was accidentally saving all my PDFs and notes and such in a group I made while trying to figure Zotero out. Well, I copied over my notes to "My Library", and triple checked they were all there. Then I deleted the group on zotero.org, and now all my notes are just gone.

Why did this happen? How does Zotero deal with moving notes from a group to My Library? I would have sworn I had all my information moved over, and yet now it is all gone.
  • What kind of notes? Standalone/child Zotero notes or PDF annotations? There are lots of PDF annotations in your personal library.
  • @GatoExpert: But if you think you lost data, you should immediately make a backup of all zotero.sqlite.bak and similar files in your Zotero data directory. If this just happened, you can likely recover from those.

    But let's first figure out what you're referring to and what happened.
  • Thanks @dstillman, I just initialized a git repo inside my Zotero folder, so hopefully the sqlite still contains it. Let me see if I can compose a more detailed response in this thread and post in a few minutes.
  • @dstillman. Here's an approximation of what I did:

    1. Installed Zotero and also created a zotero.org account.
    2. Saved a few blog posts using Zotero web clipper, and saved the associated PDFs of those posts in Zotero's default "My Library". Did some sporadic highlighting and item notes on some PDFs.
    3. Experimented with using a group to separate topics. Decided that was not the right way to go, but didn't yet delete the group.
    4. Continued to use the Zotero web clipper, which was saving (mistakenly) to the experimental group, not "My Library" as I intended.
    5. Noticed this after taking some extensive highlighting and item notes for a few articles.
    6. Dragged those articles from "Group" to "My Library", the green "+" icon showed up, so I expected it to copy those citations, PDFs, item notes, and everything I had worked on from the "Group" to "My Library".
    7. After (thinking I) moved everything, I triple checked that (I thought) the citations, PDFs, item notes, etc had been successfully copied into "My Library".
    8. After being satisfied with the above, I went to zotero.org and deleted the "Group" so the web clipper would save to the correct place in the future.
    9. Returning to the article I was just working on, and realized I couldn't find it. I sorted my entire library by "Date Modified", and my most recently modified item was not the citation and PDF with highlights and item notes that I was expecting.

    Thanks so much for jumping in so quickly! Hopefully this makes sense
  • It looks like I have a `zotero.sqlite.bak` and also a `zotero.sqlite.1.bak` for some reason. Not sure if that's normal, but it strikes me as a little strange.
  • OK, then it sounds like you either didn't copy the items or you're looking in the wrong place. Without specific examples I couldn't tell you more. To be clear, though, there are 188 items copied between a group and your personal library on December 18th.

    Dragging an item across libraries will copy it. The main exception is if you previously dragged an item across libraries, in which case it won't copy again (including any changes, child items, etc.) unless you delete the existing item in the target library, but it doesn't sound like that's the case here.

    Deleting a library wouldn't have any effect on another library.

    In any case, if you just deleted the group, you can try restoring from one of the automatic backups. (zotero.sqlite.bak and zotero.sqlite.1.bak is normal.) You'd want to copy the missing items and make sure they copied. When you then sync, it will delete the group and apply all other changes, but the newly copied items will remain in the target library.
  • Oh sorry I didn't realize you had direct access. Given that information, I think I know what happened:

    I'm specifically looking for an item titled "Introduction to the Zettelkasten Method" with around 12 item notes that collect highlights throughout the article.

    I think what happened is that "My Library" already had a copy of the item, and also the group "3.Resources" had its own copy of the same item. When I dragged the items from the group "3.Resources" to "My Library", it probably didn't copy over as I intended because "My Library" already had its own copy of the same item.
  • Yes, that would happen. It wouldn't happen in the situation you originally described, where you just saved to the wrong library and then copied that item to another library.

    Options for transferring item changes between libraries are definitely planned, but it's a hard UI problem — with the potential to wipe out existing data in the target library — so for now it just doesn't copy items that already exist.
  • edited December 29, 2022
    Woof. Are items from groups stored in the bak, or just from "My Library"?
  • Everything. I explain how to restore this above.
  • Well shoot, it looks like neither of the backups contain data newer than 12/27. At least I can get some of my stuff back, thanks anyway!
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