Selfhosted

Update in case anyone is interested: I figured out what caused the problem. When I mounted the new drive I used to store my configurations onto Proxmox, I completely forgot to make the relevant /etc/fstab entry. The drive mounted successfully so I didn't realize at the time that I had forgotten to do that step. The update I ran from apt-get included a kernel update, so I restarted the machine to complete it. Since I hadn't modified fstab, my new drive was not mounted when the system started up again. Even though the drive wasn't mounted correctly, I still somehow had access to some incomplete version of the files in its directory (no idea how that works). So no fault of Docker, LXCs or Proxmox, purely PEBKAC.

Despite getting the files back I will still work towards a more resilient system and more regular backups.

I'm not sure. All I know is that Proxmox doesn't recommend using Docker in LXCs. It seems Proxmox has much more control over the internals of the container and can break stuff.

https://pve.proxmox.com/wiki/Linux_Container

If you want to run application containers, for example, Docker images, it is recommended that you run them inside a Proxmox QEMU VM. This will give you all the advantages of application containerization, while also providing the benefits that VMs offer, such as strong isolation from the host and the ability to live-migrate, which otherwise isn’t possible with containers.

You didn’t happen to change an unprivileged container to privileged, or vice versa, after creating it, right? Doing so can break filesystem permissions, which could have resulted in something like this.

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.