This utility can erase the NOR on the EZ Flash 3-in-1. I cannot confirm that it works with other NOR-based Slot-2 cards. If you erase as little as 4 blocks, your DS will no longer show a GBA Game in Slot-2.
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)