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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.