Here m8 I did this for it to work, found this method out to work I just wrote on another forum by me, copy & pasted it over here. Don't format your MSD card I tried makes no difference your wasting your time that way, I did but this worked:-
Anyone getting fragmentation error with this rom then run this program from here:
https://dl.dropboxusercontent.com/u/94421767/gw3ds_ver_12.zip
Place the gw3ds.exe file into your C:/Users/ folder, then open CMD as Admin, type in the box:- cd C:/Users/ then trype in next, gw3ds.exe fix (Drive letter of MSD card, for example type in " gw3ds.exe fix g:") then press enter, mine found 4 fragmentation errors all from MH4 rom and after with it completed worked perfect.
Interesting. The quick format takes 1-2 seconds but copying and pasting 24gb back to the MicroSD card is a pain. Takes about 20 minutes. 1st-world problems Will take a look at the method you found.