Use TegraRCMGUI to mount the Switch's eMMC, mount it again with HacDiskMount, copy the save data and metadata, paste it into the SD card.
Boot into your emuMMC, copy the files with GoldLeaf and paste them into the correct locations. (I know this works in reverse for emuMMC->eMMC)
Heck, you can even backup the emuMMC save data, migrate your eMMC then restore the save data!
Many ways to do this though. You can make a NAND backup of both, mount the NANDs and restore the emuMMC.
Backup eMMC, boot into CFW and get the save data like that then restore it. (You can backup/restore with NxNandManager).
Make sure to have a backup of EVERYTHING, it's practically harmless but better safe than sorry.
Also, if you're going to boot into eMMC setup 90dns/airplane mode PRIOR to booting CFW. Goodluck.