There's a lot of things...

First, there's what Marcy said about reorganizing Amphibia's government in "True Colors" so that nothing like the Toad Rebellion ever happened again.

Second, there's the fact that Anne seems to have grown rather attached to Amphibia. Or as she put it, "I feel at home in a place that shouldn't be real".

That Anne feels so passionately about Amphibia as to write a song about tells me that once she gets back, she won't want to leave... especially if her parents go with her, which is all but guaranteed by the ending of "Anne-sterminator" when Mrs. Boonchuy says "whatever you have to do, we'll do it together".

And if Anne's parents are anything like their daughter, they probably won't want to leave either.

Then, there's the nature of the Calamity Box itself. It's implied that both the Calamity Box and the girl's powers originated with the Night. My guess is that when the Night is destroyed, the Calamity Box will no longer function, and the girls will lose their powers.

It's also likely that Anne won't be able to return to Earth anyway, what with the government being on her tale. Even if they're able to save the Calamity Box and use it to travel back and forth between Amphibia at will (which I think is unlikely because it's too safe a way to end the series) fighting and running from the FBI is a big deal. It won't be safe for Anne and her family to return to Earth; Anne could end up on the FBI's Most Wanted List for sheltering "aliens" once Mr. X proves the existence of the Plantars.