You should be fine to reformat, but be aware that if you had previously formatted your emunand after creating it from your sysnand image, then formatting the sysnand will give it the same ID under the /Nintendo 3DS/ folder on your SD card, so your NANDs will be "linked" again, and you'll have to reformat one of the two one more time to push it ahead and unlink them. (And that format will nuke the saved info for the other NAND on your SD card in the process, unless you take it out while formatting.)