Zotero citations linked in document but Zotero not recognizing them

dr.jackalope
Greetings,

I have been working on a manuscript for months and recently had to change the citation style. I have updated the document since changing styles, and citations were working fine (although the reference list is overlapping with line numbers, but that's the least of my problems). I opened the document to work on it today, and tried to insert a new citation. Zotero is asking me to pick a citation style and does not detect any citations (as evidenced by when I hit refresh). However, the citations do appear to be linked (highlighted gray when I click on them and the references). When I click in one of the in-text citations to add another citation, the field (where the existing citations should appear) is totally blank. When I try to add the citation anyway, it doesn't appear. I have a few screenshots that might be helpful. Any insight would be most appreciated!
  • dstillman
    https://www.zotero.org/support/kb/existing_citations_not_detected
  • dstillman
    (The citations still being gray doesn't mean all that much on its own — that just means they're still Word fields, but they're likely corrupted. The fact that it asked you to choose a citation style means the document was saved in the wrong format or otherwise mangled.)
  • dr.jackalope
    Thanks for the link. I haven't opened the file anywhere but on my laptop in Word. I've been using Zotero for years and have never encountered this problem. I just went into some older manuscripts in other folders and the citations are still intact.

    However, I just tried to open an older version of this manuscript (which also had the same name as the doc that I was currently working on) and I got an error message that I've never seen before, It looks like Word might be somehow routing my files through SharePoint (https://synergyscientifics-mysharepoint.com/personal/Jennifer_synergyscientifics_com/Documents/Documents/Synergy Scientific Services...)

    I'm not sure what's happening here because I never use SharePoint and my personal OneDrive shouldn't be involved at all. [insert eyeroll emoji X3].

    A client sent me a "read-only" PowerPoint template to edit that cause chaos on my computer today. This might be part of the chaos.

    How does Zotero interact with SharePoint? I have zero experience with SP.

    Thank you!
  • adomasven
    Zotero does not interact with SharePoint at all, but if you had accidentally saved the document with SharePoint (or SharePoint auto-saved it for you), it could have conceivably flattened Zotero citations.
  • adamsmith
    Are you able to roll back to earlier versions of the document (e.g. with Window's file versions functionality)? That would be the easiest option for fixing this rather than trying to "uncorrupt" the document. If you have content added since, you can use Word's compare document functionality to merge that back in.

    If that's not an option, I'd be curious to look at the flattened citations in more detail, but it'd be nice to avoid that, obviously.
  • dr.jackalope
    edited February 17, 2022
    Thank you for these suggestions...the plot thickens. I opened the same manuscript from OneDrive on another computer and the references were fine. Relief! I saved a new version and emailed it to myself, which kind of defeats the purpose of having OneDrive, but whatever.

    I restarted my laptop and tried to open the previous version of the file, in which the references appeared flattened and got a novel error message when trying to view a citation by clicking on an in-text citation and then "Add/Edit Citation". The error message read "We could not communicate with Zotero. Please ensure Zotero is running and try again. If this problem persists, see [address for word processor plugin troubleshooting]".

    I tried to open Zotero but it kept crashing. finally, I got it to stay open and then the references in the document were...unflattened? In any case, they work now. I think the problem is with the plugin. Could it be a compatibility issue with Windows 11?

    ETA: Also, earlier versions of the document had the same problem, but other documents created in Windows 10 did not.
  • adomasven
    We need to troubleshoot problems one at the time. If you cannot open Zotero, it unexpectedly quits or you get error messages, that's a separate issue that you should create a separate thread about and we should troubleshoot it.

    On the other hand any crashing that you see from Zotero cannot in any way affect your documents (unless it crashes while inserting a citation). It's hard to say what was the issue with your document, but as long as Zotero currently recognizes the citations it is likely it will continue to work.

    Other Zotero users successfully store their documents on OneDrive (although sometimes filenames with space symbols cause issues) without having their citations flattened, so OneDrive is not necessarily to blame here.

    If you have any other issues not related to your document citations not being recognized create separate threads and explain in full detail the issue you're seeing and what you have done so far for troubleshooting.
  • dr.jackalope
    It's all the same problem; I'm just working on a diagnosis.

    After a few more days with this issue, it is clear that there is some kind of incompatibility issue between OneDrive and Zotero. When I just tried to insert a citation in my manuscript, the manuscript (and Word itself) completely scrambled graphically. The contents of my manuscript were gone and I was not able to access the ribbon in Word at all because of the scrambled graphics. It actually scrambled all open Word documents, forcing me to close Word and try again. The manuscript opened OK, but when I tried to insert a reference, I got the following Zotero error message: "Zotero experienced an error updating your document. Would you like to view troubleshooting instructions?". When I went to the troubleshooting instructions, I noticed that one of the items was related to compatibility issues between Zotero and OneDrive for "some users".

    I will see if I can find a discussion that is related to Zotero and OneDrive compatibility issues.
  • adomasven
    If you're getting scrambled graphics, that has nothing to do with Zotero specifically. That is an OS level issue. You should update your graphics card drivers and allow the general Windows update to run, including for drivers.

    As for OneDrive compatibility issues, for some users they just cannot insert citations into documents that are stored in OneDrive, although usually only for documents that have space symbols in their filename. We have not had reports of citations getting flattened from storing documents in OneDrive.
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