Guide to Create Region Changed EmuNAND and Still Have NNID on SysNAND:
What you will need
Hourglass9 payload in sdmc:/luma/payloads named "y_Hourglass9.bin"
Decrypt9WIP payload in sdmc:/luma/payloads named "x_Decrypt9WIP.bin"
GodMode9 payload in sdmc:/luma/payloads named "up_GodMode9.bin"
Emunand9 payload in sdmc:/luma/payloads named "b_Emunand9.bin"
Part I - Backup SysNAND
1) Boot into Hourglass9 by holding "y" button at the time of boot.
2) Select "SysNAND Backup/Restore..." -> "SysNAND Backup" -> Press A to name "NAND.bin" -> Enter Button Combination to Start Process.
3) Copy all contents of SD card to your computer C:/PreFormat.
Part II - Un-link SysNAND from NNID
1) Boot into SysNAND.
2) Go to "System Settings" -> "Other Settings" -> "Format System Memory" -> Select OK to format.
3) After format console will attempt to reboot but it may fail if SD card was formatted (due to missing arm9loaderhax.bin); power off and copy arm9loaderhax.bin and luma folder from C:/PreFormat (Part I Step 3) to root of SD Card.
3) Power on console to boot into SysNAND, then go through the set up procedure as if it was a new console.
4) After you go through 3DS setup process, power off and copy all contents of SD card to your computer C:/PostFormat.
Part III - Create EmuNAND
1) Boot into Emunand9 by holding "b" button at the time of boot.
2) Select "Complete EmuNAND Setup" -> Enter Button Combination to Start Process.
3) Power Off Console, then copy contents from your computer C:/PostFormat (Part II Step 4) to root of SD Card.
4) Boot into EmuNAND by holding "R" at time of boot (Verify in System Settings you are in EmuNAND).
5) Go to "System Settings" -> "Other Settings" -> "Format System Memory" -> Select OK to format.
6) After format console will attempt to reboot but it may fail if SD card was formatted (due to missing arm9loaderhax.bin); power off and copy arm9loaderhax.bin and luma folder from C:/PostFormat (Part II Step 4) to root of SD Card.
7) Power on console while you hold "R" to boot into EmuNAND, then go through the set up procedure as if it was a new console.
8) Power off console and copy all contents from C:/PostFormat (Part II Step 4) to root of SD Card.
9) Verify that you now have 2 folders under "sdmc:/Nintendo 3DS" (This means SysNAND and EmuNAND are unlinked).
Part IV - Re-link SysNAND to NNID
1) Boot into SysNAND.
2) Go to "System Settings" -> "Other Settings" -> "Nintendo Network ID Settings" -> Press OK -> Press Next -> Press Next -> Select Link an Existing ID then follow steps to sign in.
3) Power Off Console once NNID setup is complete.
4) Copy "C:/PreFormat/files9/NAND.bin" and "C:/PreFormat/files9/NAND.bin.sha" (Part I Step 3) to root of SD Card.
5) Select "SysNAND Backup/Restore..." -> "SysNAND Restore" -> Enter Button Combination to Start Process.
6) Copy "C:/PreFormat/Nintendo 3DS" (Part I Step 3) to root of SD Card.
7) There should now be 3 folders in "sdmc:/Nintnedo 3DS" delete the one that matches the same folder name under "C:/PostFormat/Nintnedo 3DS" from SD card.
8) Boot back into SysNAND, verify you can access the eShop.
Part V - Region Change EmuNAND
1) Follow this guide
https://github.com/Plailect/Guide/wiki/Region-Changing and remember to always boot into EmuNAND at reboot and where it says "Sys" replace in your head with "Emu".
At this point you will have a EUR SysNAND and a JAP EmuNAND. The eShop will currently work on SysNAND but not EmuNAND. Note, you can never link an NNID across regions, so the one on SysNAND can only link to EUR console I'm afraid.
To fix EmuNAND eShop you can try the following (
https://gbatemp.net/threads/3ds-region-change-tutorial-easy-way.386207/) visit section "How to get on the eShop:", BUT it's risky and you can end up with an NNID ban. Also, I don't think you can have 2 NNIDs hooked up at the same time, so either EmuNAND or SysNAND will not work with eShop.
Phew! That is a lot of info, best of luck. Hopefully you will now know a bit more about NNID.