Help! Deleted directories. Did HA do that?

I’m quite new to all of this, but I had managed to get my home working the way I wanted.

I’m running Home Assistant on VirtualBox on a computer running Ubuntu. I was also running several docker containers, on the computer (Plex, Audiobookshelf, Wireguard, etc.).

I updated to 2023.6 and connected my shared media folder to HA. Cool feature. Shortly after that I realized my Roku integration wasn’t working, so I tried rolling back to a previous backup. Roku still wasn’t working, so I restored to my backup I had made just before restoring to an earlier version. The next morning I logged into Plex to listen to some music and nearly all my media folders on Ubuntu were gone, but not everything.

Everything was working, then I updated HA, added a shared folder to HA, then restored a backup, and now most of my media is missing. Is that connected, or a coincidence?

If anyone can point me in the right direction to recover this data or help me identify what might have gone wrong so I can avoid it going forward I would be very appreciative.