i promise you, you don't need to do the mid game level thing where you take away powers and lock the players in a shitty prison or sewer or whatever. you dont! no one likes these levels! they're bad, and you shouldn't make them!
metroidvanias are games about moving through and exploring an interesting non-linear space with a growing kit of tools. taking away those tools mid game and making you escape a linear hellbox to get them back just fucking sucks, every time.