All my wooden chests gone

Did you have an error when initially loading the world? If so, there’s a good chance the world got corrupted a bit, and resulted in the loss of structures and the like. I had a similar issue when I moved my world to the beta branch once and it messed up most of my caves as a result.

Make sure to look at your server_log.txt file when doing this to see if there are any issues loading it and upload that. You may have server mods that are not playing well with the update and when you branch your save please make sure whatever mods you had running to start with are present on the branch too.