I know the feeling! The fourth book I planned out for my current series around a year ago is currently looking like it's going to wind up being three separate novels thanks to various subplots taking on lives of their own and demanding more room to breathe (not to mention working better as their own thing rather than being crammed into another story).
It's hard to say what would work best without having read your books, but if the jump from the prequel to the first novel leaves a lot of big questions dangling then it might be a jarring shift. It's not a big deal for the heroine to be in a completely different situation from one book to the next (in fact, it can be a pretty compelling hook!), but it shouldn't leave the reader scratching their head and feeling like they missed a novel in between.
Does the prequel wrap up its own self-contained story arc and put the heroine in a position where she could feasibly hop into book one? Or does it leave loose ends hanging that get wrapped up off-page between the two novels?
As very general advice I'd suggest keeping the prequel as a prequel if you can, since changing a novel's place in a series after you've finished writing it can lead to some subtle rough edges here and there. For example, if you introduce a character, idea, or concept in book one expecting the reader never to have heard about it before, only to later cover the same ground in a prequel and turn book one into book two, then you can end up with some questionable bits of prose here and there that might feel off to the reader. If they're reading book two, but the author's voice is telling them that it's book one, then the overall tone and consistency might suffer. And that's the kind of thing that's really awkward to thoroughly fix in editing.