Probably a dumb question but imI going to ask anyway, if I just set up my emunand with a 128gb sd card in and I just got a 256gb card, when I copy/pasta all the files from my current card to the new one, will I have any problems booting? I know the emunand is on the switch storage but I just want to be cautious.
In general, creating emunand by default the two nands will share the same Nintendo folder. All you can do is to copy that folder to your new sd with the cfw files.
The problem is if your emunand has more games than sysnand when you download something on sysnand or just deep reboot all different games on emunand (compare to sysnand) will be deleted completely.
Solution: after setting emunand up and testing it without any issue. Boot to sysnand and do factory restore (WITHOUT MEMORY CARD PLUGGED IN) to unlink from emunand. From now on, rename Nintendo folder of emunand to NintendoEMU and sysnand to NintendoSYS. When booting to specific nand, rename the related folder to Nintendo.
Booting to a nand with the wrong Nintendo folder, the OS will ask you to delete > just press power to power of and rename the right one.