User blog comment:Plexioth- xD/Monster Hunter 3 Ultimate/@comment-76.164.105.37-20130501211902/@comment-119.93.94.59-20130503042322

You can. You just have to transfer the save back from WiiU to 3DS.

What I'm saying is... you can't play your save data on the WiiU and 3DS at the same time. It's either on or the other at any given time.