Lost a bunch of PDFs. Safe to combine old & new Zotero Storage folders to reattach?

Hi, a bunch (maybe half) of my PDFs are no longer attached in Zotero, and although I know where at least some versions of them are, I don't know the best way to get them all back in the same place. My first instinct is to copy all of the subfolders in the old Zotero>Storage folder (which is apparently not the one linked to Zotero at the moment) and paste them into the current Storage folder. I assume/hope that this would pull everything (including any notes, metadata, etc.) while still keeping any items I've subsequently added. However, not being an expert in file syncing/Zotero, I'm unsure if this is a dangerous move (and/or how it might be affected by sync).

As background, I purchased a storage plan last May specifically so that I could more easily transfer my library when needed, which ended up being important because I had a hard drive failure within months of transferring everything to a new computer. I'd followed the instructions for moving to a new computer; option A is simply to set up Zotero sync, and there were no warnings that this wouldn't allow for a complete transfer, so that's what I did. I have the 2G plan and am nowhere near capacity, so that's not the problem. It does appear that only some of my library is synced right now (~ the same MBs I'm seeing in the "current" Zotero storage folder), but I don't know which happened first - if syncing somehow removed half of my files along the way w/o me knowing, or if only half of my files were synced in the first place. The latter seems highly unlikely because I think I'd have checked that everything synced, and I *definitely* was not having issues accessing these specific files during the first few months after purchasing the storage plan (I was very actively working on my paper and accessing tons of refs at the time, through August). So, if what's showing up now as synced is all that's ever been synced, then there was a difference between what I had stored on my computer and what synced. (If you can see my sync history and confirm that a bunch of stuff disappeared somehow, I'd appreciate it, but I guess that's less of a concern right now than just getting the missing half of my files re-linked in Zotero.)

The old version of my Zotero storage (the full "Zotero" folder which I manually copied over from an external hard drive backup) - is over twice the size of the current storage folder, so it's definitely the comparatively more complete one. However, I don't want to fully replace my active Storage folder and SQLITE file with the old ones because the old version is missing things I've added in the last couple months, before I realized anything was missing. I don't think I added a ton, but still...(esp. because one of them I had to add every piece of metadata manually.) I also might have removed some duplicates at some point, although I can't really recall when exactly I did that cleanup, as it's been piecemeal (& is nowhere near done).

So is it safe for me to simply copy over the subfolders in Storage from the old to the new Storage folder, skip the prompt to "replace" any of the files, and just hope that everything, including all of the metadata and notes, if applicable, copies over successfully without overwriting new refs? I'm not sure if any of the references themselves or notes are actually missing, as opposed to just the PDFs (and it might be a while before I find out), but I suspect it's only the PDFs because the number of folders in the old Storage fodler is similar to (in fact, ~30 folders less than) the current Storage, despite being twice as many MB in size. Thanks in advance for the help.
  • Hi, a bunch (maybe half) of my PDFs are no longer attached in Zotero
    Could you say exactly how that manifests? Do you get an error when trying to open an attached file, or is there no attached file icon in Zotero at all (or something else entirely)?
  • @laurelp: Files never disappear once uploaded, so these just weren't uploaded. This would've happened because you were at your file storage at the time and never performed a file sync on the computer where the files were added after upgrading your storage. You might have stopped syncing that computer altogether, ignored the quota warning, or disabled file syncing in the preferences to make the warning go away.

    All files added since you upgraded your storage were uploaded, but that would've had to have been on a different computer that never had these files, since old files would've immediately uploaded along with any new files once you had the storage space.

    These are the 35 missing files:


    If you have these folders, I'd recommend just copying these instead of overwriting anything.
  • Hi again,

    I appreciate the response. I did try copying over those folders, although some of them didn't have the PDFs in them, and I'm still running into missing PDFs after having done that. I still don't understand how this happened because I definitely never turned off file syncing. But I've had a lot of computer problems and a couple of new OS installations/new hard drives over the last year, so it might just have to be chalked up to that. I just worry that I'm not reinstalling /copying over Zotero properly, which is why I upgraded my storage in the first place - to ensure it would go smoothly. :( And now even though I'm still dealing with missing files on my current installation, I'm about to have to go through it all AGAIN because my laptop started freaking out on me, and I'm told all I can do is a fresh Windows reinstall, which means losing all of my programs again. (I'm told my data is safe, but I'm guessing they're referring to things like my Desktop, not data within Program Files.) Any guidance on the smoothest way to do this? I followed instructions on the website on how to do it the last couple of times and clearly still managed to screw something up, so any explicit guidance/help would be greatly appreciated. Thank you.
  • All your Zotero data is stored in the Zotero data directory. If you back that up, you can restore your library to the identical state. See instructions on that page for details, but there's really nothing to it — that folder just needs to be returned to the same place.
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