Me and a friend of mine transferred his 9.5 EmuNAND (9.2 system) to his MH4U N3DS SysNAND (for legit use) just fine yesterday. It restarted the EmuNAND 3DS into sysNAND the first time and gave a "you need to update" error, but when we tried the both a second and third time it worked fine.
I highly recommend doing a PC transfer instead of the network based one though. The network based one took forever to complete (about 6GB of games on the SD card) and got an error at the end. PC transfer went fine. Restored the EmuNAND again to the original 3DS's SD card after the transfer was complete to the N3DS SysNAND.
It will be kept. I dunno how Nintendo does that, but even though the 3DS is formatted first and then restored afterwards it'll still know that you have the MH 3DS and let you redownload MH4U from the eShop.