Possible in theory. I think when you use checkpoint or similar, it gives a .fla/.eep (whatever is native for the system) as a single file.
What usually causes them to not work is the fact that the bytes/endians are all flipped around. I actually just recently wrote a tool for this, however. Here's my Github for it. Called
SaveAIO.
I wrote a special Nintendo 64 converter function that does the commonly known permutations of a save being byte swapped/endian swapped.
Since I haven't tried it in action yet for N64, I'm happy to help out. Is your Wii U hacked? If so, can you use checkpoint/saviine to dump a Paper Mario save? A completely new game is fine. Just so long as you load in, save, and exit. Make a checkpoint/saviine dump of that save and provide the zip here in addition to your Everdrive save?
Once I have it, I'll work on trying to get you some copies back to try re-injecting.