Yeah, I've noticed a user in the room above me (says he's a fully automated bot) exploiting this tactic to remain invincible.  If it uses up its last safe mode, it intentionally allows the controller to downgrade so that it can re-upgrade it and gain a safe mode back.  

It's apparently impossible to conquer the bot no matter how overwhelming my army is nor how many safe modes I'm willing to wait through.  Pretty frustrating.