Data Persistence Issue in Zotero: Deleted Files Reappear Upon Restart

CheeseyBoba
Hi everyone,

I'm encountering an odd problem with my Zotero setup and I'm hoping someone here might have some insights. I've noticed that when I delete files from my Zotero library, they seem to reappear when I restart the program. This persistence of deleted files is both puzzling and inconvenient.

Has anyone else experienced a similar problem? If so, were you able to find a solution? Any suggestions or advice would be greatly appreciated.

Thanks in advance for your help!
  • dstillman
    No, that's not normal nor something that people have reported.

    What do you mean by "files"? Do you mean items?

    Do you have your Zotero data directory in the default location, or have you moved it somewhere else (e.g., a cloud storage folder)?

    Can you make a screen recording of this happening, upload it somewhere, and email a link to support@zotero.org with a link to this thread?
  • CheeseyBoba

    https://s3.amazonaws.com/zotero.org/images/forums/u13110270/rdtl9xy1nwaswft6uwfs.png

    Picture 1 is the total number of items in my library at 5pm (it still kept increasing now)

    https://s3.amazonaws.com/zotero.org/images/forums/u13110270/3gzqz5g2bvagz7fovog5.jpg

    Picture 2 is the total number of items in my library at 12.49pm, which is my actual number of items

    Over the past few instances when I've restarted Zotero, I've noticed that several collections that I previously deleted have reappeared in my library. Initially, I deleted these collections using the "delete collection and items" option within Zotero. However, despite this deletion process, the collections persistently reappear upon restarting the application.

    https://s3.amazonaws.com/zotero.org/images/forums/u13110270/6nr0t7p8iavpbheu6ukw.png

    Now it becomes 33465 items...it kept increasing...
    Last few times it reappeared as collections so I could directly delete the collections and items, but this time it doesn't reappeared as collections, which means I have to delete all of them one by one in my library, this significantly disrupts my workflow and efficiency.
  • CheeseyBoba

    https://s3.amazonaws.com/zotero.org/images/forums/u13110270/voixnss56f1v3tsumk5j.png
    It's 42313 items in my library now, and it seems to have stopped loading, so sorry you've requested me to screen recording my issue but I'm not sure how should I screen record this, perhaps my explanation on my issue is clear for you.
  • CheeseyBoba
    Okay just now when it stopped loading, I closed Zotero and restart my laptop. Now, when I restart Zotero, the number of items is fixed at 42313, which doesn't increase anymore, may I know why is this happen?
  • dstillman
    Those aren't items you've deleted — they're just items you added in the last couple days that are being downloaded to this computer. They all exist in your online library. You can see in the screenshot that the sync icon is spinning.

    You either added these items on another computer or you just deleted your local database after syncing without actually deleting the items in Zotero, causing the items to be pulled back down when it syncs. It looks like you've done a couple different imports, which is why you also have duplicates of all your items.

    You should add the Date Added column and sort by it, and then you can delete entire batches of imported items at once.
  • CheeseyBoba
    edited May 3, 2024
    Yes, you are right, I have done several different imports and saved them in several collections.

    Specifically, I've observed that after importing or deleting items, the syncing process often takes an extended period to complete. While Zotero indicates that all items have been successfully imported or deleted, the sync icon continues to spin indefinitely.

    In these instances, I've assumed that the syncing process had completed and directly closed Zotero. Is this the reason that causes the sync may not have fully finalized, potentially leading to discrepancies in the library size.

    Could this be a possible explanation for the increasing number of items in my library?
  • CheeseyBoba
    "You should add the Date Added column and sort by it, and then you can delete entire batches of imported items at once."

    May I ask how can I implement this? But I think the main problem is that my Zotero is running extremely slow. I would like to know if there are any additional steps or best practices I should follow to optimize syncing performance?
  • CheeseyBoba
    Hi, so may I ask what should I do now? Shall I delete all items in my library and import them again?
  • dstillman
    edited May 4, 2024
    I linked to instructions above on how to add the Date Added column and sort by it in order to delete batches of items:

    https://www.zotero.org/support/sorting

    You should definitely not delete everything and import again.
  • CheeseyBoba
    edited May 5, 2024
    Alright, thank you so much!

    So in order to prevent this issue to happen again, after making changes to my library, such as adding or deleting items, I need to wait for the syncing icon to stop spinning before closing the Zotero program?
  • dstillman
    No, the problem is just that you imported tens of thousands of items multiple times, and (I'm guessing?) deleted your local database. If you're just using Zotero normally, none of this is going to be an issue.
  • CheeseyBoba
    Thanks for your response, however I would like to clarify, I haven't imported tens of thousands of items multiple times. Rather, I've been importing several files with varying numbers of citations. After each import, I verified the total number of items by summing up all the items from each files, which appears to be correct.

    However, the issue arises upon restarting the program, which results in the total number of items increasing unexpectedly.
  • dstillman
    I haven't imported tens of thousands of items multiple times
    But you did… It doesn't matter how many individual files you imported. The point is just that those files had tens of thousands of items, and you imported the same items multiple times, as you can see in the screenshots above. And you appear to have imported the same files on separate days, all on May 1 and 2 (UTC).

    Nothing "increased" when you restarted Zotero. You just imported these duplicate items in separate imports on those days.

    As I said in the other thread, you can add the Date Added column and see exactly which items were imported together.
  • CheeseyBoba
    edited May 6, 2024
    Thank you for your patience and for addressing my concerns.

    I apologize for any confusion. It seems there might be a misunderstanding regarding this.
    While I understand that there may indeed be duplicates, especially considering that I'm importing citations from multiple databases, I want to clarify that I only import each file once from my side. And each of the imported file consist items ranges from approximately 10 to 3000 items only. Consequently, even with potential duplicates, I would expect to have around 20,000 items in total rather than 40,000 items.

    Regarding your suggestion to add the Date Added column to identify which items were imported together, I've attempted this before, thanks for your advice.




  • dstillman
    Consequently, even with potential duplicates, I would expect to have around 20,000 items in total rather than 40,000 items.
    I don't know what to tell you. The items you have are the items you imported, so by definition that's how many items you imported. Zotero didn't create items on its own.
  • CheeseyBoba
    Thank you for your assistance.

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