Hi,
no, you can't and should not modify prefabs, you should only modify the instance you create with it.
maintain some variables in the fsm that spawn this prefab so that when it spawns, it can deactivate or activate a certain component on it, or have the prefab instance responsible for that, where component would be disabled by default and enabled if necessary.
the fsm on the spawned prefab can enabled disable any component on itself or on any object it's given, by maybe the fsm itself is disabled, which then is logical that it can't do anything.
Bye,
Jean