This.
It is VERY important that you do not log in with your NNID on your new 3DS before you do the transfer. When going through initial setup, tell it you don't want to set that up! If you do, apparently when you do the transfer the first step will be to totally format the target system because there's no way for it to merge eshop data between two NNID's. If you do the transfer the correct way, what will happen is that it will just delete what's on the SD card for the new 3DS, and merge all of the eshop data from the new system with your NNID, including the MH4U game.
I haven't gone through the process myself, but that's my understanding of it. If you do mess up and accidentally put your NNID on there and try to do a transfer, then sadly you will need to call Nintendo and hope they can reinstate the game.
However, as Vyse mentions, you will be required to redownload the game as the game itself will be deleted from the SD card (just not the license).
This is why I wish they would have just provided a download code instead to redeem on the eshop or something. Thie system transfer stuff is pure shenanigans!