Hi! I was in a similar boat wherein I bought my Switch Lite on SXOS v3.1.0 on sysNAND (HOS 11.0.0) secondhand and wanted to migrate to Atmosphere emuNAND. Given that you're SD says 499GB capacity then I'm guessing you're on sysNAND too. Here's an outline of the steps I did to migrate to Atmosphere on emuNAND. Keep in mind that you will not be able to run XCI files once you're on Atmosphere.
In SXOS, you can check whether you're on emuNAND or sysNAND by going into Album and checking if there's "EMUNAND" written on the logo on the upper right, like in the photo below.
If you have SXOS on sysNAND, then you need to check whether Incognito was applied to your sysNAND. You can check by going into System Settings > System > Serial Information and checking if the displayed serial number is either
blank or
XAW00000000000. If it is either of those, then Incognito was used on your sysNAND, and you need a backup of your
prodinfo.bin (on my Switch Lite on SXOS that I bought secondhand I thankfully found it still on my SD card in
/backup/prodinfo.bin). Put your
prodinfo.bin in
/backup/prodinfo.bin.
Once you have your
prodinfo.bin in
/backup/prodinfo.bin, make sure your switch won't connect to the internet (Turn Autoconnect off, use Airplane Mode, or delete your internet settings altogether), then run Incognito (
https://github.com/blawar/incognito/releases/latest) to restore your serial number.
Once you've restored your serial number to your sysNAND, you can follow this guide (
https://rentry.org/MarikoEmuNAND) to setup Atmosphere on emuNAND. If you're sysNAND HOS was ever updated with ChoiDojourNX then you might need to do this guide (
https://rentry.org/SwitchFAQ#error-fatal-error-nxboot-couldnt-parse-boot0) as well (fortunately for me, I didn't have to do this). You should now be able to use Atmosphere on emuNAND.
Assuming you've
never been online on your dirty sysNAND (guy who sold me the Switch Lite told me it has never been online), and
if you want to be able to boot into stock OFW on your sysNAND without getting banned (not 100% confirmed, but it's worked for me so far), then you need to clean your sysNAND. The way I did this is emulating the steps Haku33 does but with Lockpick_RCM, NXNandManager, and Hekate. First,
make a backup of your current sysNAND in case something goes wrong (
https://rentry.org/BackupRestoreNAND). Then download Lockpick_RCM.bin (
https://github.com/shchmue/Lockpick_RCM) and place it in
/bootloader/payloads/ on your SD card. Boot into Hekate and launch Lockpick_RCM via Payloads > Lockpick_RCM.bin. Then select Dump from SysNAND with the power off button. Once your keys are dumped
and you're still on the screen where it says "Wrote XXXX bytes", press and hold the power off button until it powers off (normally I think pressing the power off button and using Vol+/Vol- to scroll in the menu will work, but I ran into a glitch when I tried this on my Switch Lite and the volume buttons weren't working). Then, copy the
/switch/prod.keys file in your SD card to somewhere on your computer and move the
/Nintendo/ folder on the root of your SD card into
/emuMMC/RAW1/Nintendo (this is the Nintendo folder that is exclusive to emuNAND). Make sure the
/Nintendo/ doesn't exist in the root of your SD card anymore. Then extract NXNandManager (
https://github.com/eliboa/NxNandManager/releases/latest) to somewhere on your computer and run the driver/dpinst_x64.exe executable to install Dokan's driver. Place your SD card back into your Switch Lite and boot into Hekate. Then go into Tools > USB Tools > Set Read-Only to OFF, then click
eMMC RAW GPP and plug your USB-C cable into your computer. Run NXNandManager and go into Options > Configure keyset and get your keys from the
prod.keys file you copied into your computer. If NXNandManager reads the keys successfully, then you're good to go. Otherwise, Lockpick_RCM failed and you need to try and dump the keys again.
Once NXNandManager is able to read your
prod.keys file, then we can now begin cleaning the sysNAND. Keep in mind that
this procedure will remove everything in your sysNAND and you will be left with a "fresh" (like stock) sysNAND.
Mount your SYSTEM partition with NXNandManager, and go into it using Windows File Explorer and go into the
/save/ folder. To be safe, set your File Explorer options to be able to view hidden and system files. Now,
except for 8000000000000120, 80000000000000d1, and 8000000000000047, delete everything inside /save/. Next,
unmount the SYSTEM partition and mount the USER partition, and
delete all of these folders inside: Album, Contents, save, saveMeta, and temp. Now,
make new empty folders for those folders that you've just deleted. Inside the newly created and empty
Contents folder,
create two new folders: placehld and registered. Unmount the USER partition and close NXNandManager, and unplug your USB-C cable. Go back into Hekate's main menu and select Reboot > OFW. You should be taken to the screen wherein you setup your Switch for the first time (date and time, users, internet connection, etc).
Congratulations! You now have Atmosphere on emuNAND, and a clean stock OFW sysNAND you can use for playing online, browsing the eShop, etc. You can update your stock OFW sysNAND via System Settings, but you might need to run Warmboot Error Fix from Hekate > Launch the next time you boot.