Saves will need converting to either R4/m3dss or RAW (aka supercard GBA slot, g6 and EZ4), use shuny's coversion tool/site should you lack the means to do it otherwise:http://shunyweb.info/
I don't have a wii u anymore to test it myself, but if homebrews are not visible on the wii u menu I think you can press L + R + minus to open the plugin menu, there should be an option called "homebrews on wii u menu" or something similar
Or when your player dies, you can say in code, if enemy exists, do nothing, but if enemy does not exist, then create enemy at certain spot. (This would be a pain tho for lots of emeies)