Ray,
The machine e-stop will not stop the current head rotation. It will stop any machine motion after the head has indexed. An e-stop is not necessary to stop the machine though because when the machine tries to move a 'probe not armed' error will prevent automatic motion.
If the module is knocked off during rotation and the head continues to index into the part you will get an 'overload' or 'datum' error. If this allowed to happen you will shorten the life of the head. Therefore great care should be taken when debugging programs that clearance for head index is OK.
Duncan.