Once I alter one of my abilities with a Mutagen, is it like equipment where I can go back later and switch it out for a better one? Or is it a permanent change to that ability that I'll keep for the rest of this playthrough?
Mutagens cannot be reversed nor replaced. Once applied they cannot be upgraded either.
So if you have a lesser version of some mutagen, you might want to wait for the greater version and sell everything until then.
Personally, I find it a bad design decision.