I'm confused with this as well. I've only just needed a prefab now so haven't touched them.
I've made a prefab in the project tab and created an instance, and something seems to be messed up. Ie, the prefab I've just instantiated is immediately different to the prefab itself. I'm not sure if there's a bug with undo or the way I was trying to use Unity's Select/Revert/Apply instead of Playmaker's? (PS, where IS Playmakers Apply feature? I've changed things on an instance and wanted to apply it to the prefab, but how?)
So my prefab is in the Project, I drag into Hierachy, and I look at the action of the prefab instance. Prefab instance has different actions. I tried changing the FSM name and instancing, which works, but the actions within the FSM are still not matching the prefab.
After deleting that prefab and 'redoing it' it seems fine. However I also tested a change where I changed a variable in an action, hit revert, and it didn't actually revert that variable. If I add an extra action, change the variable and then revert, then the new action vanishes and the variable reverts! Odd!
Thanks,
Jay