*edit-
Garro posted a simpler solution for digital versions of the games using savedatafiler
Cart saves are still totally unknown though it would be great if somebody with the same issue with a retail cart, could backup their save using powersaves and edit the save using a hex editor without changing anything and then just re-import the save and see if it's successful?
Garro posted a simpler solution for digital versions of the games using savedatafiler
Instead of deleting the whole save file you can just go to the save data and press X+R I think? The option that says "delete secure value" and after that inject the save, it works for ORAS at least, so it should work with Animal Crossing.
Cart saves are still totally unknown though it would be great if somebody with the same issue with a retail cart, could backup their save using powersaves and edit the save using a hex editor without changing anything and then just re-import the save and see if it's successful?