Nope, but you should make a backup of both your SD card and your emuNAND (using emuNAND9) just to be safe.So I don't even have to format my sd card before following the guide?
You'll also need to backup of your sysNAND at some point, the guide will instruct you when to do so.
No, if the behaviour has changed, it's more than likely a result of a firmware update. The easiest way to find out is to switch back to reiNAND.Back on ReiNand i didn't have this problem so i figured it must be Luma3DS.