Very little is as disappointing as conquering a holding with a unique building and just having it sit there, disabled, for the entire rest of the game because you're the wrong religion. While there are a handful of events that allow you to convert specific buildings for use by other religions, I think it should be a more general mechanic as it was far more common historically to repurpose such structures than to just let them sit there, unused. Alternatively, choosing to let them remain in use as sites for their original religion should give popular opinion bonuses/bonuses with minority vassals or the like.
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