Articles deleted from references and library after update

I updated Zotero yesterday. When editing my bibliography in Word with the Add/Edit Bibliography button, approximately half of my references were removed from my reference list and entirely deleted from my library. When I closed that window and returned to my manuscript, those references were no longer listed. When I attempted to re-add the references by redoing in-text citations, the articles did not show up as options to cite.

This is wildly inconvenient for multiple reasons. At a minimum, how can the removed articles be restored in my library? They are not in the trash. It is as if they never existed in my library.
  • edited October 11, 2022
    This is some sort of misunderstanding.

    Updating Zotero wouldn't cause you to lose data, and items being removed from your library wouldn't cause entries to disappear from your bibliography anyway.

    When using the Word plugin, the bibliography simply includes the citations you've inserted into the document, so you should be able to delete the bibliography and reinsert it to get the exact same bibliography you had before (barring any edits, which generally should be avoided anyway).

    Your online library shows a total of 5 items deleted over the course of four different days in the last week, presumably by you. Nothing else has been removed.
  • edited October 11, 2022
    Hi, yes, there does seem to be a misunderstanding!

    This all happened last night. I deleted the five items in my trash prior to this and none had been in the manuscript, so those are unrelated to this issue.

    The references that were removed from my bibliography are not showing up in my library or trash whatsoever. In Word, I did delete the entire bibliography and attempt to reinsert it. However, it reproduced the bibliography with missing references, exactly as it was before I deleted it. The in-text citations for the missing references are now only text, as if I had manually typed them in and they had never been linked to any reference in my bibliography. Prior to all of this happening, because I was in the final stages of editing, I had only hit the refresh button to make sure everything was current. I didn't manually edit references or citations.

    For example, I know the following article should be in my library and this paper's bibliography, but it is in neither. I cannot add it as a citation or a reference, because nothing shows up when I search for it in the citation window or the add/edit bibliography window. It is also not one of the articles in my trash.

    Clarke, G. N. et al. (1999). Cognitive-behavioral treatment of adolescent depression: Efficacy of acute group treatment and booster session. Journal of the American Academy of Child & Adolescent Psychiatry, 38(3). doi:10.1097/00004583-199903000-00014

    Thanks for your help!
  • edited October 11, 2022
    I'm afraid you'd have to be misremembering some part of this. What you're describing isn't possible.

    1) You're using syncing, that item doesn't exist in your online library, there's a record of items deleted from the online library, and you're saying it wasn't one of those 5 deleted items. There's no other way for items to disappear from the online library. So that means it never existed in your synced library.

    2) Citations becoming flattened would cause them to disappear from your bibliography, but that has no connection to items existing in your Zotero library. Even if you disabled syncing, added items, added citations to your document, deleted the items, emptied the trash, and re-enabled syncing (none of which happened, obviously), you would still just have orphaned citations with embedded metadata in the document, and they would show up in the bibliography.

    I can really only think of two possibilities:

    A) You added those citations as plain text at some point with a plan to add them to your Zotero later. They wouldn't have ever been in the bibliography in that case.

    B) You had them in a different Zotero installation on another, unsynced computer, you added them to the document, you saved the document in the wrong format and caused the citations to become flattened, and then you opened the document on this computer and added additional citations from this Zotero. At that point the original items would've disappeared from the bibliography and been replaced by the new citations linked to the database.
  • edited October 11, 2022
    Perhaps this is a new bug that hasn't come up before? Issues aren't always on the user's side. Microsoft Word also released an update recently and possibly something with the Zotero plug-in is now glitchy. I've never experienced issues with Zotero before and neither of the two possibilities are what happened.

    I only write on one computer, which is synced, and the articles were undoubtedly in my library with annotations and notes. I often reference the article I included in my previous comment, so I am positive it was in my library. After Zotero glitched, my paper went from 43 pages to 36 pages. References in my bibliography were the only content removed from the paper, and those articles are no longer in my library. It isn't just like one or two articles that I manually cited and forgot to upload to Zotero or had never downloaded in the first place. That wouldn't have been worth asking for help for.

    Nonetheless, I appreciate you considering what may have went awry and your prompt responses. Thanks for troubleshooting.
  • Perhaps this is a new bug that hasn't come up before?
    Right, bugs absolutely happen, but this would be like 5 massive, unrelated and highly improbable bugs in three separate pieces of Zotero software (Desktop app, Word add-on, and Server) occurring at the same time and not reported by anyone else -- you'll understand that's not super plausible.

    It's still possible that something went wrong, including possibly due to a bug, but even in that case, there's with near certainty something that you're either mis-remembering or that's missing from your description.

    Do you have an old version of the Document with (some of) the now missing citations? Either a version you emailed, or a local backup, or using Windows file versions or Mac time machine?
  • Yep. @venanzld, the only other thing I'd add to what @adamsmith said is that it looks like you only started syncing on September 29, despite using Zotero for a few months before that, so if something happened to your items before that date — say, if you accidentally deleted a collection with all its items (and emptied the trash or let the trash auto-empty after 30 days) — then they wouldn't show up in the server logs. But that still wouldn't cause citations to become flattened in the document, because the plugin just doesn't work that way. So this is still almost certainly a case of misremembering something.
  • @adamsmith yes, I do have an old draft with some of the citations before they were flattened and removed from my bibliography and library. Where can I send it? Thanks for looking into this more!

    @dstillman that's true I only started syncing recently and accidentally deleting things before then is definitely not outside the realm of possibility. I double checked a value in the Clarke article yesterday though, so that doesn't apply in this situation. Also, I did a lit review over the weekend for the revisions I worked on yesterday. Aside from the Clarke article and one other, the missing articles were uploaded over the weekend. Procrastination gets the best of me, and I am confident I am not misremembering which of the missing ones were newly added to Zotero. I also use the Zotero Connector extension to save articles to my library, so if there's any accessible log of that or way it could be implicated, feel free to investigate further!
  • edited October 11, 2022
    You can send the file to support@zotero.org with a link to this thread and a list of some of the missing items.
  • Great, sending shortly. Thanks!
  • The document you sent has Paperpile citations, not Zotero citations.
  • edited October 11, 2022
    Oh god, you're right. I had started the paper months ago with Paperpile then transitioned over to Zotero. Looks like the user was indeed wrong!

    I still don't understand why the above problem happened now and articles were deleted from my library, since I've added a lot to the paper and made many bibliography and citation edits with only Zotero since then. That's helpful info either way, and I guess the reason is irrelevant since two citation managers were involved.

    Thanks for your help with this. Whatever went wrong provided a good reason to revise and switch all remaining citations and references over.
  • edited October 11, 2022
    The items weren’t in Zotero — at least not since you started syncing — and Paperpile citations never would’ve been in a Zotero bibliography. You’re just misremembering this.
  • At this point, we can agree to disagree about me misremembering the articles being in my Zotero library. I had exported a RIS file of all articles in Paperpile, added that file to my Paperpile folder on Google Drive, then imported that entire folder to Zotero. Anyways, thanks again for your help throughout this! I'll see how things work out when any remaining Paperpile citations are replaced with Zotero ones.
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