This is a little disheartening, as I spent a lot of time organizing saves into various projects and things.
I do backup routinely, so I think I might be able to restore most of them, but will have still lost data. I also lost all saved objects in my chest. Hopefully I can just replace the directories with a backup.

All I did was update a low priority linux python patch on linux. Open TTS, run
/networktickrate 30
/networkpackets 1
I flipped a table and the game cold froze, so I had to use xkill on it.
And that's it. I didn't change any other behavior. What could have caused a random wipe of my saves? My log file is 21kb. I have to reduce it to upload it. Could you perhaps increase the maximum log file size for the forum?