Ok - I gave the hotel another call and asked to speak with an assistant manager this time. They were able to refund the duplicate charge after confirming that they do see both charges. They also expressed that it's not typical that modifications would result in a cancel/new reservation so it was a probably a glitch with the migration. Moral of the story is that the systems are crazy right now, and you might need to escalate to a hotel supervisor or manager to get things resolved, but the reps have all been very understanding and apologetic about the less-than-smooth transition.
Last edited by TravelLawyer; Sep 6, 2018 at 12:57 pm