When lava spawns inside a stronghold due to how Fire Stone Ore replace function works it has a good chance of replacing a End Portal Block in a strong hold. This makes the entire stronghold useless. I figure if the conditions are right other elemental stone replace functions can do the same. Suggesting add a black list of blocks that can't be replaced/ just make it so they can't replace End Portals.

Hey there! Thanks for submitting this report. Is there any chance that you'd be able to provide the seed to the world that you noticed this in?

Was in one of my countless test worlds (I can look for it but will take some time)

If you're able to find it at all then that would definitely be helpful; I've spent a decent bit of time trying to find an example of this bug myself but have come up shorthanded thus far.