Amiibo figures are compatible with a range of Nintendo games, but can only hold data for one title at a time.
"Amiibo can only store data for one read/write compatible game at a time," Nintendo of Japan has confirmed.
"If you wish to use the data from other read/write compatible software, please erase the data in the 'Amiibo settings' section of the Wii U settings menu."
Luckily, that doesn't mean you can't use your Amiibo to unlock bonuses in games other than the one you're currently porting around data for. So if you've got Super Smash Bros. Wii U data on a particular Amiibo, it will still unlock the respective special content in Mario Kart 8 and Hyrule Warriors.
A third and fourth set of Amiibo figurines were announced this week.