I have an Anbernic RG351P and the only complication was that I had to partition the card for the firmware and ROMs. That's not going to be the case for all of the handheld consoles out there, but be sure to check for your specific Retroid model.
Having firmware on the SD card is unique to Linux handhelds. Android handhelds are basically phones so the operating system is in the flash chip on the motherboard.
Just copy all the contents of the SD card over to be safe. Retroarch might be storing files on the SD card and the BIOS folder might be separate from the ROMs.
There's a few Bios files I know are in the roms folder, but everything that isn't in the main android directory is in its own ROM folder, and I mean everything.
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