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Not even on reboot, it just get's deleted somehow, been happening for the past couple of months and I haven't been able to figure out why yet. I posted all about it here (https://lemmy.world/post/32756942) if you are interested in reading about it.
Do you have the media cleanup plugin installed for Jellyfin? I wonder if you change the PUID and/or GUID if you couldn't make sure Jellyfin wasn't the source of the deletion.
I don't have that plugin from what I can tell, and I did not install it manually either. What should I try changing the PUID and GUID to?
I would think the Jellyfin logs would say if it deleted something. But I have to say, I cannot fully understand GUID and PUID in all cases. But you can try to subtract 1 digit from PUID (100 to 99) and then try to delete a show or movie within Jellyfin's interface. If it won't do it, then you've got the permissions at least where it can't delete things. It is possible to not view things as well, so it might take some research or trial and error and make sure you write down where it is now. But, it will remove one factor at least.
Finally caught it! It was Jellyfin stupid ass deleting my media!
Fuck yeah! One issue down, 9,374 to go!