This is something that has bugged me for years now, I searched for an answer and could not find it so I hope it's not a dumb question.
Back in the day I abused the sheez out of the Box tricks in my pokemon gold cartridge, specifically the fusion glitch.
This involved no glitch pokemon, neither eggs, so its not the
unstable hybrids bulbapedia has documented.
The closest I could find is this but 1) In my case, only 1 pokemon survives and more importantly 2) The daycare wont "cure" it (I remember triyng with mewtwo and not succeding, at least, but I could be wrong in the last point. Also, maybe the timing had to do with one dying or not, but that's not the point).
In short it's the clone glitch but instead of swaping boxed pokemon with the party ones (like you would when cloning), you would swap places of 2 pokemon in the box. If you had the right timing when turning off the system, the result was one pokemon dissapearing from the box, whith the other "absorbing" his data like EVs, genes, moveset and the like. I used it to get stuff like shinny graveler with surf and sacred fire and the like.
The joke was that the recipent pokemon also absorbed the donor's sprite. The fix was to do this on a pokemon that could evolve, as evolvining changed its sprite.
Even then I assumed the donor was giving all his unique data to the recipent, while the recipent mantained it's species since it retained it's type(s), could still learn its regular lvl up moves, evolve normaly... but the sprite is the thing I can't wrap my head around. Why would the sprite be corrupted when clearly the pokemon species/ID/whatever is intact?
Since all stats and stuff are recalculated when taken outside of the box, I'd assume storing individual sprites for each pokemon would be out of the quesion. I looked up on bulbapedia an it also says the sprite is linked to the species, and from a database design standpoint it's also the logical choice unless you plan on giving at least 2 pokemon of the same species 2 different sprites, like with event pokemon a la star-eared pichu. But there is no such thing in gen II as far as I know.
What was happening?
EDIT: Nvm, I learned from one of crystal_'s videos that the game actually stores the pokemon species in 2 different places at the same time; so probably I never tried with the daycare at all.