never had a problem with multiple rooms resort fee waivers at HR Tahoe or Andaz Mayakoba.

if resort fees still on folios checkout morning, then i'd go down early checkout morning to see the folio on the 1st room and get resort fees removed.
then, checkout later in the day on the 1st room via app

checkout in person on the 2nd room as leaving the hotel, get 2nd room resort fees removed at that time.