No, no issues would happen and nothing would break if you follow this:
1. Grab emuNAND Tool 1.0.3 (works for Windows)
https://gbatemp.net/threads/emunand-tool-release-and-support-thread.359239/
Steps for your current mSD card:
2. Take out mSD from console and connect it to your PC through a card reader.
3. Copy all files and stuff from the drive that shows in Windows to a folder on your PC (includes Nintendo 3DS folder and files in your root directory... basically everything)
4. Run emuNAND Tool 1.0.3 and click on "Extract emuNAND" button, save the emuNAND.bin somewhere on PC. Let it complete till 100% and wait few seconds after it completes just to be safe.
Steps for your new mSD card:
5. Put the GW launcher.dat on new mSD and insert it in your console, run the exploit as usual to go to GW launcher menu and select "Format emuNAND" (it will create the hidden emuNAND partition the same way as your previous mSD has).
6. Turn off console, take out mSD card and now connect this one to your PC, delete all contents from new mSD (like Nintendo 3DS folder if there is any) and copy back the contents that you backed up from your previous mSD to this one.
7. Run emuNAND Tool 1.0.3 again and this time click on "Restore emuNAND" button and select the emuNAND.bin that you backed up from your previous mSD.
8. All done! Put the new mSD back in your console and everything should work as it was with your previous mSD.
PS. Recommended SD card size for O3DS is 16GB max. and mSD card size for N3DS is 32GB max. And to be safe keep the previous SD card and don't format or delete anything from it until you are sure that the new one is working fine.