no. ingame protestant religion is a collection of subspecies ;-)

but will conversion catholicism/protestantism possible?
you mean faction conversion? for example baiern goes to protestant? no.

only one faction could possible change, but it is a spawn faction, so AI Faction. And the event who triggers spawn inludes the decision which religion.
if you mean people conversion, sure, if you build protestant church in Munich also the bajuwars will leave roman slavery :-D