Help- highlights and annotations disappeared (using Zotfile)

natnicks99
Some of my papers in my Zotero library, that I definitely remember reading and highlighting (although can't remember if I ended up making the annotations into a note) seem to have disappeared. When I open the file, it asks me for the file location- the file is under the usual filepath, but then when it opens it lacks my highlights. I've lost a lot of work this way!

The one thing I've been able to do is to download SQLite, and by opening the zotero sqlite file, I can see my annotations listed in a CSV, under "item annotations". But these annotations don't seem to be linked to any paper...

I did that because I followed the instructions here: https://forums.zotero.org/discussion/92343/annotations-deleted-after-using-zotfile
It was mentioned that restoring highlights after that is "a breeze"! But I don't understand what to do next...

Any help very, very much appreciated.
  • dstillman
    When I open the file, it asks me for the file location- the file is under the usual filepath
    Can you be more specific? What's the exact message you're receiving, and what do you mean by "the usual filepath"? If you're talking about a File Not Found error, that means you don't have the files on this computer. You appear to have been at your file storage quota and are still at exactly 300 MB despite having upgraded, so most likely you haven't yet synced any of the files above that limit from the computer where they were actually added.

    In any case, that wouldn't affect annotations made within Zotero. What's the zotero.org URL when you click on the parent item of one of the affected PDFs in the web library?
  • natnicks99
    Sure! I have a folder that I save any PDFs I download, and this is the same folder that I have set up as the PDF saving location for Zotfile- that's what I meant by the usual path.
    The error I get is :

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

    (filepath)

    It may have been moved or deleted outside of Zotero, or a Linked Attachment Base Directory may be set incorrectly on one of your computers."

    I think that that issue is because I have periodically reorganised my file structure. However, if I then find the file in a slightly adjusted filepath, that PDF doesn't have my highlights on...

    This is an example of one of the affected PDFs:

    https://www.zotero.org/natnicks99/collections/NQQY99LL/items/EMGAMGAR/collection
  • dstillman
    edited July 5, 2023
    That PDF has 49 annotations.

    To be clear, you need to be opening the exact same file (or else the annotations might appear in the wrong places) and you need to be opening it in Zotero's built-in PDF reader. The annotations won't appear in an external PDF reader.

    We can't help with the file paths. That just means you did something that caused them to be unlinked, which is part of the reason we don't recommend using linked files and don't provide any support for linked-file workflows. But the PDF reader works exactly the same with linked files.
  • natnicks99
    edited July 5, 2023
    Sorry my mistake, I linked to one that was not affected!!

    https://www.zotero.org/natnicks99/collections/NQQY99LL/items/9GUFQ9K7/collection

    https://www.zotero.org/natnicks99/collections/NQQY99LL/items/MZKHPMTF/collection

    I didn't realise that about linked PDFs, that is good to know. So it is likely to be an issue with the linked file?

    Do you know whether there is any way to restore my comments that I can see with SQLite?
  • dstillman
    You're just looking at the wrong file. (You have six copies of it in your library.) The item with the attachment that has 24 annotations is TF5IUNWP. You can paste it into the Zotero search bar in All Fields & Tags mode to find it.
  • natnicks99
    Wow! That's so great, I thought I'd never find them again!
    Can you explain how you went about finding the right item, so I can replicate this process for other papers?

    For example, I think that this one should have annotations?
    https://www.zotero.org/natnicks99/search/jackson/titleCreatorYear/items/BM5MKT4G/item-list

    or this one
    https://www.zotero.org/natnicks99/search/jackson/titleCreatorYear/items/FV5YJ64Z/item-list

    Also, do you know how I've managed to end up with so many copies of the same files? Is this because I've put them into multiple sub folders? I'm trying to avoid this issue again...
  • dstillman
    Can you explain how you went about finding the right item, so I can replicate this process for other papers?
    I looked for other attachments in the library with a similar filename.
    Also, do you know how I've managed to end up with so many copies of the same files? Is this because I've put them into multiple sub folders?
    No, not at all. That doesn't duplicate items.

    You have multiple copies because you added multiple copies to your library. You had multiple copies of the same file both under separate parent items and under the same parent item. (ZotFile might have contributed to the latter, trying to convert between stored and linked files, though it doesn't create multiple copies by default.)

    To avoid future confusion, you should merge duplicate parent items and delete duplicate attachments, being sure not to remove the attachments with annotations.
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