First, I hope that this was a TAPPS game because under UIL rules there are no provisions for a running clock. Second, as you say, even if the R incorrectly directs the game clock to run, the play clock rules do not change. And finally, the B may give the 1 or 2 hand pump up signal to communicate with the R, but only the R can officially decide to reset it. If the R doesn't give the signal, don't reset it.