User blog comment:Kogath/Monster Hunter 4 Ultimate for the Nintendo 3DS/@comment-6974847-20140923011615/@comment-5449468-20140923151957

I would think it's like:

1. Start MH4G. 2. MH4G searches for MH4 data on the SD Card. 3. MH4G converts a copy of these data into MH4G data. 4. Play MH4G with your old hunter and material.

I don't think that there is a difference between the card and the E-shop version.