Even if its in bridged mode you can screw it up by adjusting one side at a time while the unit is on.... I used to have a 2-ch MTX amp running the same way.. cranked up one of the gains.. and throws off your entire amp... bridged or not..
Your output from the amp is still 2-ch... even in bridged mode.. cranking the gain on one side.. causes an electrical imbalance.. or something along those lines.. and can throw excessive volts through the one side to the sub and back into the other channel..
This is one reason I hate amps that have independent gains on a 2-Ch...