When updating this server, all player data is lost (not including stats). It looks like the username.dat was converted to userid.dat, but all data is missing and replaced and loads default in the game. This includes all items in your inventory as well as experience and current location. You are started out at your spawn chunks with an empty inventory.

On further inspection, it appears as though the new userid.dat file contains the items in your inventory, but they are not being loaded into the game when updating the server.