I refer to you my other post from above:
If you backup your save data again, is the other save the same size as your *hax save file?
My guess is that save manager only restored as much of the save file as it could and not the whole thing.
That, or there are some OoT cartridges out there with bigger save memory chip for whatever reason.
Edit: I just tried here too, 2.5 payload with the *hax save file, the system.dat file, and a save01.bin. svdt gives me the error pictured above, save manager just crashes with a message I can't read because it returns to HBL before I can see it.
In both cases, it doesn't give me the *hax save file and another save file to play.
Oh, you're using the eShop version. That probably changes things. eShop version probably has more space available for save data. Are you able to restore a third save file too?