You can boot with your new media, than run the ceemmc tool and make a backup of internal install (storage) only.
Then you can manually copy the data from the backup (the tool tells you the location) to the root of the storage partition on a PC.
Or you create a backup like kostaman is talking and just remove the internal install with ceemmc.
The steps for a firmware upgrade are described in the how to. And it’s without loss of any data.