Losing the relationship with some pdf files over 3500 references: a Zotero limitation ?

Hi ! Being a French obstetrician involved in research, I use Zotero since 9 months on a recent Mac, without any worry since recently. Today my Zotero version is 5.0.55.1 and my Library has 3941 references corresponding to a Storage of 6793 files (9,67 Go).
I save from time to time my references on Zotero Site (pdf excluded of course), and both my Zotero Storage and my pdf files (separately) on my Mac and external Hard Drive. No displacement of the Zotero Storage file has been achieved.
But, since recently (and more and more) when i click on some formerly introduced references, the corresponding pdf is not found. This a not tragic, as I saved also all the pdf involved in order to find these quite easily, but it is slightly fastidious. Mainly, I have the feeling than the more I will enter references with related pdf and the more other pdf relationships will be lost. Quite disappointing ! So my questions are: 1) Has someone as much a over 3500 references in his Library ? 2) What is the best solution for further acquisition (as I will certainly need over 10 000 references in the future ...)
Thanks by advance for the exchanges.
  • Nothing to do with library size, and not a bug in Zotero. There's no way for a local PDF to go missing without deleting the attachment item in Zotero, so either you (or something else) deleted or moved the local file or the file was simply created on another computer that wasn't fully synced.

    https://www.zotero.org/support/kb/files_not_syncing
  • Thanks so much for that quick answer !
    Strangely I am quite sure that I always added references and files properly on what you call Computer A and the updates on Computer B in the right chronological order etc. Of course what I mean is that pdf relationship is missing for a certain number of references on Computer A.
    Taking into account your indications, I can not yet see any solution.
    I suppose that the answer to my question 1 is that many users have entered even more references than me.
    I suppose also that taken together the size of my Library without pdf will never reach 300 MB, even in the future with more than 10 000 references. Even so, it would not explain my current problem occurring in Computer A.
    So what I intend is to continue my Zotero acquisitions same way, to achieve even more attentively each step, and to look forward if more and more formerly introduced references no longer keep their relationship with attached pdf.
    In any case, I will inform the forum on the evolution
  • Again, there's just no code in Zotero to delete files from disk without deleting the attachment item, so something else would have to be going on.

    If you provide a Debug ID for opening an attachment that's not found, we might be able to tell you more.
  • Double clicking on one of the numerous mysterious lost pdf relationship give the following Debug Journal yo already received
    D1332247125
  • (2)(+0000008): Attachment file '/Users/[…]/Zotero/storage/VIHG4HJL/[…].pdf' not found
    So this is a stored file, and the file doesn't exist within the 'storage' folder in your Zotero data directory.

    However, it looks like you have ZotFile installed, which would generally suggest a linked-file workflow. (You also have no files synced, as would be the case when using linked files.) I'm not quite sure how you have things set up, but it's possible that ZotFile is moving your files elsewhere on your system but somehow the attachments aren't being properly turned into linked files.

    You should check your ZotFile settings.
  • Thanks again ! And bravo ! Indeed I installed Zotfile some months ago.
    My Zotfile settings seem to have been modified some weeks ago without my willing*. Currently in General Settings the option "join in Zotero a saved copy of the file" is ON.
    So since this modification, the latest pdf files could be joined in Zotero Site, so I may have reached the 300 MB limit. So the preceding files could have been erased in Zotero Site. Precisely the lost relationships are limited to a precise period compatible with this reasoning.
    So I suppose I have to move the Zotfile option into Personal Folder "Zotero Storage" ?
    I suppose also the Recovery Procedure will be tough and "one by one" ?
    * Or maybe my Zotfile setting are wrong since the Zotfile beginning (some months after beginning using Zotero without Zotfile).
  • edited October 2, 2018
    This has nothing to do with file syncing or your storage quota. You’re nowhere near your quota, no files in your personal library are synced, and in any case Zotero doesn’t delete local files unless you delete the attachment itself. This is some issue with ZotFile or other steps you’ve taken, not with Zotero itself.
  • Being not able to find the mistake in configuring Zotfile, I consider the option of uninstalling Zotfile. If you agree with the idea, can I simply remove it in the Tolls Addons window ?

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