The only issue I've seen is if you have installed games to internal nand, some of those games can get corrupted if u switch to an SD card that has a different Nintendo folder setup.
However, the games that have installed to SD card seem to work fine. Everything shows up on home screen, but games not on current SD show up as available in cloud. And when you swap SD cards, the opposite games show up as available in cloud.
Just be careful if you have games installed to internal nand, they may get corrupted. Unless you know which folders in "Nintendo" folder to copy on to both cards.
If anyone has come across this and knows why else it may be happening, or how to prevent it, let me know...