As Nial pointed out, your provinces are more likely to revolt when you're ex-comm'd.

You also touched on another aspect: other catholic factions will eagerly attack you,alliance or not, because it's open season on your heretic butt...you'd notice this more immediately if you were on the continent, say as the Germans, surrounded by French, Poles, Danes, Hungarians, etc.

Several times (as the Spanish) I've had to fight my way to the pope and kill him (which cancel's ex-comm's) just to settle folks down.

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