Accidentally attached all my PDFs as Copies - Want them to be links - how to undo this safely?

Hi All,

I've just started using Zotero and I love it so far!

However, I used the drag-and-drop method at the start on my PDF library before I started working on bibliographic metadata.

This means Zotero is now storing huge redundant PDF files on my harddrive - copies of PDFs I already have - and making it impossible for me to manipulate the Zotero files in the way I want (I want to be able to make backups on a flash drive, just of the metadata. But the Zotero data directory now contains thousands of GBs of my own PDFs by accident).

I want to delete all of these redundant extra PDFs, without losing any of the bibliographic metadata I've attached them to. How can I do this without endangering my metadata?

Best wishes,

  • If you just want to delete the files, you can do an advanced search for [Attachment File Type] [is] [PDF], create a saved search from that, do a Select All to select all the files, and press Delete to move them to the trash, and then empty the trash.

    But that will remove the PDFs altogether, so you'd have to relink every PDF to its parent item, which seems like it would be prohibitively tedious.

    If you've added all of your PDFs to Zotero, you have a couple other options:

    1) Just try letting Zotero manage your storage, which is what we generally recommend. Zotero provides more options for searching/organizing/tagging, you can double-click an item in Zotero to immediately open the PDF in your preferred PDF reader, you can generally still drag attachments straight to email or other places (or use Show File to get to the file itself), you can delete unwanted items in Zotero and have the PDFs deleted instead of having to manage files separately, and you can even use a saved search in your OS to get a view of all PDFs within the 'storage' directory if you really want to use your file manager. And it's easy to get those PDFs out of Zotero later if you want to. This also gives you the option of using Zotero file sync to access those files via web/mobile or on other devices without setting up syncing another way.

    2) If you really prefer an external file structure, you can use the ZotFile plugin to convert all the stored PDFs to linked files in a new directory, using a renaming scheme set up in the ZotFile preferences, and then delete your old directory. (I'm not sure if bulk-renaming is currently working in ZotFile, though.)
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