University computer migration broke links to files - PLEASE HELP

I was using zotero with the zotfile plugin for managing my linked pdf files (academic papers). I had linked attachments with the base directory set to
and the files were stored in

The university migrated our computers to a new internal system, and they have replaced BoxSync with Box drive. I got my computer back from the IT folks, reinstalled zotero and and zotfile, and changed the base directory to:
and set the path for zotfile renaming and moving to

Yet when I click on any item, it gives me the "File Not Found " error. Can anyone please help me? I have 2,500 items in my library and it is not feasible to manually locate each of those files. I am in sheer panic mode. Thank you in advance!!
  • I had linked attachments with the base directory set to
    and the files were stored in
    The whole point of the base directory setting is that it should point to where your files are stored, so that the paths can be stored as relative paths. If you store the files outside of the base directory, they'll just be stored as absolute paths, and if you move them they'll no longer be found.

    If I'm understanding what you've done, you should be able to fix this by temporarily creating a C:\Users\[username]\BoxSync\Desktop\Zotfile_Library, copying all files there, setting that as the base directory (which will convert all the paths to relative), and then changing the base directory to back to C:\Users\[username]\Box\Desktop\Zotfile_Library.

    You can also just install the Zutilo plugin and modify all the attachment paths in batch that way.

    Either way, once you've fixed it, you should make sure that your base directory is set to where the files are actually stored.
  • Thank you for your reply, @dstillman I had both the Zotero storage and the Zotfile_Library with the pdfs in the same folder (i.e., Desktop). I didn't realize that I should have had BoxSync\Desktop be the base directory instead of BoxSync\Desktop\Zotero, which I would have just changed to Box\Desktop. When you explained, I immediately realized my mistake. Zutilo was a lifesaver!!! :)
  • One followup question, if you have the chance, @dstillman

    I want to have the same zotero on my home and my school computer. Can I point to the same Box\Zotero storage on both machines for the data library? (and the same Box\Zotfile_Library for the linked pdfs)?

    Thank you! :) :) :)
  • You absolutely shouldn't store your data directory in a cloud storage folder. If you want your Zotero data on multiple computers, you should use Zotero syncing.

    It's fine for the linked attachment base directory to be in cloud storage.
  • Sorry to keep asking questions @dstillman but I'm confused... My work and home computers don't have the same paths to Box... so if I were to have the data directory on the computers, instead of on Box--wouldn't the relative links be different, making it impossible for me to have access to the linked files on both computers? I do use Zotero syncing, but I didn't think that kept the relative paths etc...

    The reason I want the linked files is that I like to be able to access my pdf journal articles from anywhere--without having to have zotero or papership downloaded since that's a real nuisance...

    I was using this person's recommendation:
  • edited August 27, 2019
    The paths are relative to the linked attachment base directory, not to the data directory. The data directory is where the database (zotero.sqlite) is stored, and that's what absolutely can't be in cloud storage.
  • edited August 27, 2019
    It says this on the page you linked to:
    Under “Data Directory Location”, leave it set as your profile directory. The profile directory does not contain any files you need to mess with, and can remain hidden. The one thing you must never do is put this directory in a DropBox (etc.) folder; that will corrupt your database over time. Just leave it happy where it is.
  • @dstillman I suppose I'm not understanding what "base directory" and "data directory" mean... I have what I think is the data directory in Box\Desktop\Zotero and the linked pdf files in Box\Desktop\Zotfile_library -- what would be the base directory in this case?
  • I linked to a page that describes the data directory, and as I say, that's the folder that includes zotero.sqlite. You can't put that in Box.

    The linked attachment base directory, if set, is the directory that Zotero uses to make linked file paths relative so that they can work on multiple computers with different file structures.
  • Thank you @dstillman I think I'm just confused about what my folder structure needs to be for the links to work :/
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