Ideally you'll want (if you are the host) to send all files to a volunteer, that can check if the troops were ordered or not to move in the .ORD file of your opponent. If no and they do move, then I would be as surprised as you!
About switching ON or OFF the AI when playing a PBEM. This is not necessary. Unless you don't read in-game messages
When you want to run a turn and your opponent file is not there, then the game tells you that the AI will take over his turn. You don't want to do that, but you have got a warning telling you that things are not ok.
IF on the other hand you have switched off the AI and forgot to add the turn of your opponent, then I think you won't get any message, as the AI won't want to take over, and then you'll run the turn without the input of your opponent. This can perhaps mean that moves planned some turns ago will still be underway, and this can lead your opponent to believe he has troops moving under their own will whereas this is a normal situation.