Broken Links, 4000 grey'd out PDFs, I can't make online sync, Zotfile, nor Zutilo fix it

Markingham
I am in crisis because I have passed an academic deadline and suddenly lost links to all of my PDFs. I can relink them one at a time, but that takes forever when I have over 4000 files. I tried using Zutilo, but it won't work.

My PDF all lived in a single Onedrive folder where I had moved them using Zotfile. I had paid for unlimited Zotero storage, which was a lot for my student budget. Do I understand correctly that because I moved them using Zotfile, they are not actually backed up by Zotero, and so paying for unlimited storage isn't helping me?

I think I messed up by having my files live in two different custom places on two different computers. Since my laptop screen cracked, I had moved my files to another computer. I had set up Zotfile on the other computer to point to a new folder for all the files. I did this because I didn't want to risk overwriting the original files, or ending up with two copies of every file in a single folder. But having my files live in two different folders seems to have caused a conflict in my Zotero account.

I have looked at many threads and tried several options (such as Zulito), but nothing seems to work except re-linking each file one at a time (which would take me over a hundred hours with over 4000 files). Can someone please help me? I'm in trouble here, years of work is at risk, and my deadline is past.

Thank you! -Mark
  • dstillman
    Do I understand correctly that because I moved them using Zotfile, they are not actually backed up by Zotero, and so paying for unlimited storage isn't helping me?
    Yes. Zotero Storage is for stored files, not linked files. And as noted in that link, we can't provide support for linked-file workflows, which are much more error-prone and which we don't recommend.

    But from the sound of it you just haven't set your Linked Attachment Base Directory correctly.
  • Markingham
    Thanks for this quick reply. I returned to my secondary computer, and it seems that most of my files are still accessible there. So, I am returning them to stored files and syncing them up to the Zotero cloud.

    To restore functionality on the computer in which all the pdf's are grey'd out, do I uninstall Zotero and then install it fresh, allowing the files to sync down from the Zotero cloud? It says in a forum that this is not recommended, but I'm not sure how else to do it.

    If I then access the files on two different computers when they are stored locally on each computer in the Zotero folders, will they sync properly?

    What particularly concerns me is that I use Drawboard to mark up my PDF's--this being a very important part of my academic research process. When I change a PDF that I access through Zotero, and then save it, the file would get bigger. Does Zotero recognize the change and upload the modified copy up to the Zotero Cloud? Mendeley did not do this, so I was forced to have all of my files in a folder that I backed up myself so that I would not lose the hundreds of hours of time I spend making margin notes, underlining in my own colour-code, etc., but that I would also not loose my links.

    If I had to start over with a fresh version of Mendeley, I had to make sure that files were named identically, and then replace the files that Mendeley downloaded from their cloud with the ones that I had customized with marginalia. That way I got to keep my hundreds of hours of customizing of the files, as well as keep my hundreds of hours of updating meta-data by continuing to have my modified PDFs synced properly.

    What is your advice on how to best manage this process using Zotero.

    I had been using a MS Onedrive folder to house all of my Zotero linked files. Is Onedrive as problematic as the rest (Dropbox, Google, etc)?

  • dstillman
    To restore functionality on the computer in which all the pdf's are grey'd out, do I uninstall Zotero and then install it fresh, allowing the files to sync down from the Zotero cloud?
    No. If you convert linked files to stored files (Tools → Manage Attachments), you can just sync normally.
    When I change a PDF that I access through Zotero, and then save it, the file would get bigger. Does Zotero recognize the change and upload the modified copy up to the Zotero Cloud?
    Yes. It's no different from using an external PDF reader to annotate the PDF.
  • tim820
    edited April 1, 2023
    To be clear, you didn't really 'mess up'. As stated earlier, you just needed to complete the setup for your new computer - since PDFs are at different locations on each computer ... that is, set the Linked Attachment Base Directory under Edit\Preferences\Advanced\Files and Folders on each computer.

    Then Zotero would know where to *look* for your PDFs on each computer. On the other hand, Zotfile's Custom Location just sets where PDFs get *put*, when downloaded by the Zotero Web Connector.

    Onedrive is not really problematic for linked PDF files. Nor is Dropbox, Google Drive, etc. Those are only problematic for the Zotero *Data* Directory Location (ie where zotero.sqlite is stored).
  • Markingham
    I also really like that when I have all of my files in one folder, they are easy to search out files that I need offline from Zotero, just using windows search once windows indexes it.
  • dstillman
    There's nothing specific about linked files for that. From Stored Files and Linked Files:
    If you prefer to find files without going through Zotero, you can use your operating system's search features (e.g., Spotlight on macOS) or create a smart folder in your OS to show a list of all PDFs within your Zotero data directory and interact with the files directly.
  • Markingham
    Thanks for all the help on this. My second computer that I had moved file to did not have they grey'd out. I reverted all of those files back to the way Zotero likes it (stored files). Then when it was done uploading all to the cloud, I checked the cloud. The cloud no longer had grey'd out pdfs. Then I shut down that computer and opened up the computer that had almost all pdfs grey. I hit sync, and gradually all was restored. Now all is well again. I lost 1.5 days, but I'm happy all worked out.

    I'll have to look into smart folders. That might be the way for me to leave the files stored where Zotero wants them, and then also gain the functionality to all the indexed content that I want all in one simple place. I have an extensive library of over 4000 PDF's along a variety of my research interests. It is great to be able to do searches of my own entire content portfolio--sometimes I find great connections.
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