Wiping out the file like that seems a bit extreme for a problem with the actual file. Crashing, locking up, sure, but erasing itself...

I'm wondering if he's dropping the remote or something... Prontos are well-known to not like that very much. It's also possible there's just something slightly off about the remote - ie. a cold solder joint, or some aging component, that makes it occasionally generate an error that ends up corrupting a few bits, enough that it decides to failsafe itself with the backup file.

You need to create a teeny tiny version of your configuration and load it into the backup space, so when it reverts he can still control the system.