Well, that is indeed something that shouldn't happen in any circumstances on a healthy device. What you copy on a flash disk must stay there by any means. That explains also why there was an issue writing building folder. On a wince devices like Mio, only registry values (if are changed) goes to default state on every boot, but that is not important in this case. I think there is a hardware failure, most likely faulty flash disk..I'm sorry but at this point I'm afraid that I can't help you any further.

as a last resort you can (slow) format entire flash disk and than try again, copy files back and try again. But first you need to make a backup to your PC first.