Broken links between "storage" folders and Zotero database

lbharrington
Hello, I have a large library, with >2,000 citations included. In summer 2025, I got a new computer. I moved my Zotero library and files to my new computer and have been using it since then, but my PDFs that I've saved over the years appear to have come unlinked.

When I navigate to the Zotero-->storage path on my computer where PDFs are stored and I open an individual folder, I can see that a PDF is there.

Then, if I go to Zotero to try to see where it's looking for the PDF, it shows me it's looking in the same "Zotero-->storage" but the random assortment of 8 letters/numbers is different (which tells me it is looking in the wrong spot). The trouble is, my computer doesn't contain a folder with that random assortment of letters.

I cannot reimport the PDF, because Zotero seems to "think" it has the PDF even though it's grayed out and gives me an error when I try to open it, saying "The attached file could not be found at the following path...[path]...It may have been moved or deleted outside of Zotero, or, if the file was added on another computer, it may not yet have been synced to or from zotero.org."

Does anyone have tips on what I should do? >2000 references is too many to go relink via these randomly assigned strings of letters. And, I cannot seem to reimport the PDFs because Zotero thinks it has them even though it cannot open them. Tips very welcome!!

https://s3.amazonaws.com/zotero.org/images/forums/u14203551/gxseyg971o26p8asv281.png
  • dstillman Zotero Team
    It's not looking in the wrong spot — it's looking where the file was when you added it. As the message says, either the file was moved or deleted outside of Zotero or was added on another computer and not transferred/synced properly to this computer. You don't say how you transferred your data to this computer, but you're at your free file-storage quota, so if you used syncing, you likely had many files that didn't transfer because they were never uploaded to Zotero servers in the first place.

    If you still have your old computer, you could either copy all the 'storage' subfolders to this computer or add a storage subscription and sync:

    https://www.zotero.org/support/kb/transferring_a_library

    (You might see another copy in your 'storage' folder from a group library or duplicate. Those are totally separate items, and they don't mean Zotero is looking in the wrong place.)
  • lbharrington
    Thanks for responding. Unfortunately I do not still have my old computer so that is not an option. When we moved files from my old computer, we copied the Zotero subfolders, so I'm not quite sure what we did wrong. If helpful, I am also noticing now that the PDFs (at least the random ones I've looked for) ARE indeed on the Zotero web-based version, with the correct 8 character string that holds the real PDF on my C drive. So they are openable there on the zotero app, but not on my desktop app.

    So, if I add a storage subscription and sync, do you think that this problem will be fixed?
  • dstillman Zotero Team
    edited today at 5:02am
    Again, there are no "correct" and "incorrect" 8-character names. You're just looking at different attachments. For the missing ones, if the files were openable in the web library, they'd be openable in the desktop app too unless you don't have file syncing enabled — Zotero always tries to download a locally missing file. Again, you're at your free storage quota, and the vast majority of your files were never uploaded to the online library because you don't have the space for them.
    So, if I add a storage subscription and sync, do you think that this problem will be fixed?
    No. Adding a storage subscription doesn't cause files to somehow appear on our servers that were never there to begin with. That would just allow you to upload them from the computer where they were actually added and still exist.

    (Can't tell you what you did when you copied the files, but I'm afraid you didn't copy them to the correct place. You can search your new computer for those folder names and see if they ended up somewhere else.)
  • dstillman Zotero Team
    edited today at 5:01am
    (I would guess that you copied everything to the wrong place and the only files you can actually open are the ones that fit under your 300 MB quota and are being pulled down from the online library. So it's worth trying to find the files you copied elsewhere on your computer.)
  • lbharrington
    Thanks! I'm also wondering if there's a way that I can instead get the grayed out PDFs that are showing up on my desktop app to go away, so that I could newly pull in the PDF again. Right now I haven't figured out how to newly pull in a PDF that I'd had before, because Zotero looks like it has a memory of having had it (even though it doesn't have access to the file location where the PDF is anymore) - but I can't open it. It has me in a bind, since I really can't use Zotero to read my PDFs anymore in the current state.

    I'd be happy to pay for the storage if this would fix it - but it sounds like unfortunately that may not do the trick for me at this stage. But maybe could save me in the future from this happening again.

    I'll do some looking on my computer for the 8 character strings to see if I can find the files - good tip. Thanks.
  • lbharrington
    Yes, unfortunately I am doing some searching for a few of the 8 character strings that Zotero is looking for, and it's not finding them. So, again, I'm not sure what we did wrong when we transferred files, but it looks like we don't have them on this computer.

    If I accept this as what has happened, what would you recommend as next steps to get a large library back to functional again, where PDFs are openable? I think I could 1) pay for storage); 2) have Zotero look for PDFs by running in the background while I do other work; 3) relink anything it can't find by me finding them by hand.

    But I'm a bit stuck with how to go about these steps and find the full text of these articles because I'm seeing a grayed out PDF image and no "find full text" option for these articles when I right click. I only see "find full text" for articles that I never pulled the PDF in for before. I welcome any ideas of how I can remedy this at this point.

    Thank you for your help! I appreciate it.
  • tim820
    The Attachment Scanner plugin can help you find (tag) items with missing attachments.
    https://github.com/SciImage/zotero-attachment-scanner
Sign In or Register to comment.