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That's pretty weird, where were the files stored that went missing? Just in your home folder?
Definitely recommend setting up regular daily backups, you can use the built in proxmox backup system, or run whatever tool you want inside each VM/CT.
The files were on a mountpoint, completely separate drive. This has also been the case for all the previous times I ran an update, though I did recently move these files to a different drive mounted the same way. I got some sort of permission wrong maybe?
Will definitely set up a better backup system as soon as I can
Very odd, I think something else is going on not related to LXC/Proxmox. I've got LXC containers with external mounts and internal storage and haven't seen any data loss over the years they've been running.