Format the 128GB card to FAT32 using literally anything other than windows own format tool. Windows has an artificial restriction built in for formating to FAT32 - probably to benefit the exfat aliance they are in - or to prevent stupid users, from formating their big harddrives to FAT32 and then complaining, that they cant be using tha big files...
Gui Format for example:
http://www.ridgecrop.demon.co.uk/guiformat.exe (see:
http://www.ridgecrop.demon.co.uk )
The rest should just be a matter of copy/pasting files. I've have no experience with emuMMC yet - but regarding everything else, thats the correct approach.
Copy directly from sdcard to sdcard using windows preferably (using MacOS does change some folder flags, which you dont want to (Hekate doesnt 'make it right again' with the Nintendo folder option). Linux maybe (not tested).
Thats all that should be needed.
(If you have two partitions on your sdcard because of emuMMC - yes cloning would be the way to go - then expanding one of them presumably. In which case - asking what filesystem should I go with is irrelevant, because if you clone one - you already take over the filesystems of the partitions of the source one.)
If you are using emuMMC and want to screw up everything already - lust for exfat.
I havent read even one emuMMC guide yet, but even I know that all emuMMC stuff is fat32 bound - and that the internal nand uses fat 32 as well - so why does the person that actually did an emummc conversion know nothing about it? Havent you read anything? Using others to do all the work for you again? Following videos?