Can't happen
1) I did an backup#1 of my sysNAND 9.2.0.20E, also all the files from the SD cart
2) Then created a new stock one with format my emu- and then sysNAND, configured the 3DS from scratch, only the needed parts
3) Made again an backup#2 of my new sysNAND, also 9.2.0.20E and made an backup of the new created files off SD cart
4) Then flashed the last sysNAND backup#2 to my emuNAND
5) After that I launched HBL with ninjhax2 on emuNAND
6) Installed menuhax on emuNAND
7) Made an backup#3 of my emuNAND which is holding the menuhax cooldboot right now
8) Flashed the emuNAND backup#3 into my sysNAND wich is then holding the menuhax
9) Flashed the sysNAND backup#1, my original NAND with all my stuff on it to my emuNAND
Yeah I know a littl bit complicated, but I started yesterday with this stuff, didn't even read about something like the cold boot because I aways but my Gateway in and bood from go.gateway-3ds.com.
But I didn't want to do that all the time especially if there is no WiFi
So please forgive me about this complicated steps, I'll learn right now