Being removed from the Sysnand yeah. From the Emunand, it shouldn't.
You could try reinstalling Devmenu to the Sysnand then copying the dbs folder from your mSDs Nintendo 3DS > Sysnand code > dbs to your Emunands code folder. I don't know if this would solve your problem though. Just a guess.
My systems not unlinked for some reason. I followed the whole tutorial and once mset was set up I removed the SD and formatted the system memory. Then plugged the SD back in once everything in the initial setup was finished, and for some reason the Emunand is still sharing the same folder as Sysnand. I've even tried this again and still their linked. I will try restoring my original nand via Gateway, and see if I can unlink them this way.
The only other thing I could think of is I'm using a 64gb SDXC card, but it's formatted to FAT32 so I fail to see why this would be the reason :/