Check the friend code in emunand/sysnand, if it's different then the NANDs are unlinked.
Another way to check is by looking the Nintendo 3ds folder in the sd card. If you find 2 folders with numbers/letters + a folder named private then you have unlinked NANDs.
Like the previous post says if you have o3ds / o3ds xl / 2ds with rxtools then it's safe to update emunand, if you have n3ds / n3ds xl then no, don't update, but you can use reinand instead of rxtools and update to 10.5 emunand.