To start with I would get a second charecter setup, one for his own world and one for yours. At least then he can run with a slim gear set on the jumping profile and if it bugs it wont be a big deal. He can always hop back into his world to grab a new gear set. Best case for this is if he can get his world progression one boss/biome ahead of yours so that he can bring second rate gear that is easy to replace in and if it gets lost no biggie.

Aside from that, look into setting up Windows (or the mac equivilent if you are on it) file recovery up. Set it to backup the save data directory on both machines, then if you run into issues with either person you will have local backups.

As to the cause (or how to avoid it) not sure... If you have a spare PC in the house look into hosting a dedicated server for your world rather than local hosting, it tends to be more reliable in many ways and less laggy!