File path pains

drvjburton
Hello,
I use Zotero on both my work and home laptops, and recently had to move my PDFs from my hard drive to SharePoint storage due to work-imposed restrictions. I must have made a mess doing this as it has broken file paths and I get many 'The attached file could not be found at the following path: ...' messages now. I long ago met my sync limit. Is there any way out of this mess? What is best practice for managing storage? I can't really pay for more.

Thanks for any advice!

Victoria
  • dstillman
    edited July 25, 2025
    (Just to clarify, the "best practice" would be using Zotero Storage. While someone from the community might be willing to walk you through debugging problems with linked files, that's an advanced configuration, and we specifically aren't able to troubleshoot problems with such setups.)
  • tim820
    edited July 25, 2025
    Usually the clue to fixing linked file path issues is in the error message - where Zotero thinks the file should be - compared to where the file actually is now. If the problem is simple, setting a Linked Attachment Base Directory on all your computers should solve it. But don't do that until you understand the exact nature of the path problem.

    Your Zotero online file storage quota is irrelevant to linked files, as linked files can't be synced by Zotero. And data syncing is free and unlimited. So the actual file paths to linked PDFs - which are stored in that data - can always be fully synced across computers.

  • drvjburton
    Ok, so I have been following the error message which is still on my C drive, and updating them manually, which is tedious, I naively assumed it would automatically update them, like my previous software. I will look into how to update the paths. File paths are the bane of my life it seems.

    Thanks for clarification on storage Vs linked. Wish I could afford to store them with Zotero, sadly they have to go on SharePoint.
  • tim820
    There is almost never a reason to update many file paths manually.

    What is the file path listed in one of the error messages now ? And what is the actual path to that file ?
  • drvjburton
    For example,

    The attached file could not be found at the following path:

    C:\Users\victb\Zotero\storage\TUFZBV7V\Jensen et al. - 2025 - .pdf

    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 zotero.org.


    Actual:
    C:\Users\victb\Natural History Museum\Victoria's literature - Documents\Literature\storage\TUFZBV7V

    The file path on my other laptop will have a different username though.

    I didn't realise that Zotero creates a folder called storage, I had been keeping a PDFs in folders per journal in C:\Users\victb\Natural History Museum\Victoria's literature - Documents\Literature\ as per my previous software Mendeley

    Oh dear what a mess.
    Perhaps I should start over.
  • tim820
    edited July 25, 2025
    So Zotero must have initially stored that PDF at C:\Users\victb\Zotero\storage\TUFZBV7V\Jensen et al. - 2025 - .pdf. Because that's how Zotero recorded its location. And Zotero still thinks it is there.

    And that is a 'stored' file (not a 'linked' file) - as shown by the path being Zotero\storage, followed by an arbitrarily named folder (TUFZBV7V) that Zotero created for that particular PDF. So as it stands, I am not sure now that you have 'linked' PDFs. You would have had to have done something to convert stored files to linked files, and I am not seeing where you did that. Broken file links do occur most often with linked files. But we may have jumped to that assumption prematurely.

    How exactly did the PDF - that must have once been in the above TUFZBV7V folder - come to no longer be at that location, but instead now be physically located where you say it is now ?: C:\Users\victb\Natural History Museum\Victoria's literature - Documents\Literature\storage\TUFZBV7V\Jensen et al. - 2025 - .pdf
  • drvjburton
    Ok I must be confused between stored and linked files then. I had thought I was used Zotero to organise my PDFs on my C: drive (C:\Users\victb\Zotero\) as I was doing with Mendeley before it, but recently had to move all my files to a Sharepoint folder (C:\Users\victb\Natural History Museum\Victoria's literature - Documents\Literature\) which I assume what broke it.
  • tim820
    edited July 27, 2025
    OK, so if your data directory was originally at C:\Users\victb\Zotero\ that makes sense for Zotero thinking the example PDF should be at C:\Users\victb\Zotero\storage\TUFZBV7V\Jensen et al. - 2025 - .pdf (that PDF's stored path at the time it was originally saved in Zotero).

    If you simply moved your storage folder (and all the folders under it) in your OS to
    C:\Users\victb\Natural History Museum\Victoria's literature - Documents\Literature\storage, then Zotero had no way of knowing that you did that. Which is why it still thinks PDFs are in their original location.

    Is that what you did ?
    (which would confirm that "linked" files are not part of all this ... except maybe for any single-PDF broken paths you may have "fixed" by linking to the individual PDF at the new file path at your Sharepoint location).

    So the first solution - to restore Zotero's ability to find all your PDFs - would be to move your storage folder back to its original location. If you have many PDFs and you don't do that, you'll be in a world of pain to fix all your broken PDF file paths. Try it for a few PDFs first to make sure that it works - that is, Zotero can find the PDF again.

    Since Sharepoint is a cloud service, you cannot put your Zotero data folder in such a location, nor anything under it, like the storage folder (since there is no way to tell Zotero that you have different locations for those two folders).
    https://www.zotero.org/support/kb/data_directory_in_cloud_storage_folder

    The only possible *relatively simple* solution I can see for you to avoid using Zotero file syncing (since you have exceeded that quota) AND use Sharepoint for *just* your PDFs would be via your OS, not Zotero. You would symlink the Zotero\storage folder hierarchy from its standard location to a Sharepoint location. If you don't know how to do that, you would have to get someone from IT to show you. If you do that, make sure it's all documented, because you'll need to set it up the same way on every computer you use.

    Your only other options are WebDAV syncing (of the default "stored" files), or converting all your PDFs to "linked" PDF files (usually via a plugin like Zotmoov or Attanger), with their limitations ....
    https://www.zotero.org/support/attaching_files#stored_files_and_linked_files
  • drvjburton
    Ah bother, yes that is what I did. I will move it back on my personal laptop to see if I can fix the issue before finding a more permanent solution, since we are not supposed to be using C: to store any files on work laptops. Thanks for the help!
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