@sugarfree sounds like I'm going to be out of luck then :(
Can't back up the current memory, as I don't think you can really do that unless you're a dab hand with forensic style tools (I'm certainly not!)
Would hot swapping the flash drive possibly work? As in, if I remove the drive and plug in a different one, would RetroArch write to it on exiting the emulator? Or is the mount restricted to a specific disk identifier?