Your mistake if planning to use the Firenzecard was making reservations for the Uffizi and Accademia: you do not need reservations if using the card, and probably couldn't have made those bookings without buying tickets. From the FAQ of the card's website:
http://www.firenzecard.it/index.php?option=com_content&view=article&id=20&Itemid=119&lang=en
"You don't need to make any reservations with Firenzecard, except for the Dome (Cupola). For the Dome (Cupola) the booking is required - you have to make it at the ticket office in piazza San Giovanni 7 after the collection of the free ticket. Firenzecard lets you visit the museums when you want to and you enter directly into the museums through the reserved entrances. Just go to the priority access following the “Firenzecard” signs and show your "physical" or "digital" card to the staff of the museums. In case of digital Firenzecard, you have to enter the "Museums" section of the App Firenzecard, choose the museum you want to visit and click on "start the visit" to obtain your digital ticket."
No idea if you'll get a refund.
Here's what you need to do for the Borghese (from the FAQ section of the website):
http://www.romapass.it/en/FAQ/
"For the Borghese Gallery and Palazzo Valentini (Domus Romane), the ticket reservation is required, but free for Roma Pass 72 Hours and/or Roma Pass 48 Hours holders.
"Please note: for reservations to the Borghese Gallery and/or Domus Romane/Palazzo Valentini, please call +39 06 32810 (open Monday to Friday, 9:00 am to 6:00 pm – Saturdays, 9:00 am to 1:00 pm) or send an email to [email protected].
Bookings can be made directly from the visitor’s home country, even before purchasing the card. For reservations by email, booking confirmations will be provided within 48 hours.It is highly recommended to book at least 10 days in advance. You can make a reservation even if you are not in possession of your Roma Pass card yet, always providing the name of the Roma Pass holder."
