Sure they can file a 498a in future. If you can’t figure out what has changed, move cautiously. The FIR can be quashed by filing an appeal in the High Court. Let them take the initiative and pay for it. If there are no kids in the marriage, their grounds for troubling you and your family in the long run were very weak and they probably realize it. Watch out for it. They may want to settle back their daughter so that she can conceive and then start harassment again. Get a lawyer involved in getting the agreement document done. If possible, get her and her family to admit in court that the FIR was false. Difficult to do, but who knows, you may get lucky. And if her intentions to live with you are genuine, then there should be no hesitation.
All in all move cautiously and slowly. Time and patience will disclose if there is an ulterior motive or not. And don’t jump at cohabiting soon. Take a few months. Let the cases close and then decide.