There's other ways I'm more a fan of for migrating emuMMC, I should have a guide about it on this site sometime later. Only leaving this up for those who wish to use Hekate to backup.
Having an emuMMC hidden . This will back up your emuMMC hidden partition NAND, it's what has your games installed on the emuMMC, save games, and switch firmware. Make sure partition already on your SD card.
Ideally, 32GB of free space to back up your emuMMC in one shot, if you have less than 32GB of free space you can refer to this page.
Step 1. Download the latest build of Hekate.
Step 2. Open
hekate_ctcaer_X.X.X_Nyx_X.X.X.zip and extract the
bootloader folder to the root of your SD card (this is what we'll use to back up your NAND.)
Step 3. Boot your switch by injecting the
hekate_X.X.X.bin payload to your switch.
Step 4. Tap on
Step 5. Tap on
Backup eMMC. This is where you'll find different options for what you can back up.
Step 6. Tap on
SD emuMMC Raw Partition, make sure it says
ON. After tap on
SD eMMC BOOT 0 & BOOT 1. These are always needed in conjunction with your emuMMC NAND backup.
Step 7. Tap on
Close once the backup finishes. May take a minute or two. Close will be greyed out until the backup finishes.
Step 8. Tap on
eMMC RAW GPPSD emuMMC Raw Partition is still set to
Step 9. Tap on
Close once the backup finishes. Note that this will take half an hour or so. Once it's done you can tap on
Close in the top right. The option will be greyed out until it's done.
Step 10. Power off your switch, plug the SD into your computer or however you do it.
Step 11. Copy the
backup folder elsewhere on your computer. Delete it after from your SD card.