doubtful. the system shouldn't update if it updates the conventional manner it should error on you. afaik, the update folder is just a temporarily folder much like the import folder for games and such. that content is then sent to its destination. I"m not sure what would happen if using a game though. a game update may not even touch the update folder. you can always recreate the folder. if you're paranoid about it. I"d suggest staying on 5.5.1 if you can. there's no real reason to update unless you want to hinder yourself.
thanks for your reply, I won't take the risk.