that only stops any future mods from being set to your Pokedex, doesn't remove existing entries.
You should re-enable it, then:
then re-import all the stuff in your box (so that those get set into the Dex) then disable it.
probably because you cheated without knowing what you were doing
For the Chesnaught, your Pokédex probably has it set like this:
The displayed setting value isn't the same as seen value, so if you cheat badly, it's possible for that to occur.
As I've said, no one ever reported this issue before. You probably screwed up your save somehow.
Maybe you'll get banned, maybe your Bank subscription gets cancelled, maybe nothing happens. No one knows.
For the record, back in Gen 4, when people had Arceus in their dex before it was officially released, those players get blocked from going onto GTS,
so at the very least, we know that GF/Ninty has done stuff by checking the dex before. (tho, there is no indication they are doing that now)