Hi, hopefully I'm posting this in the correct place/format, because I'm at a loss.
So I hacked my Switch, and wanted to experiment with SV save editing. I started a Pokémon Violet new game, and immediately gave myself access to a bunch of Legends Arceus Pokémon, all items, all Miraidon abilities, and all Fly points on the map.
I had a Cyndaquil before I even picked a Paldean starter. Fun!
I then proceeded to play the game entirely legitimately, never edited the save again, just blitzed my way through the story with my items/money/supercharged dragonbike.
Strangely, I'm noticing that certain things wouldn't load. I was unable to unlock the Judge function until several weeks after beating the League - the PokéCenter nurse randomly gave access one day. But there are still some issues. I transferred my save back to my unhacked Switch so I could battle online, etc, and noticed I was never able to Surprise Trade. There's always "something wrong with the Pokémon I selected", even if it was freshly caught. I also appear to be unable to find current 7-star raids.
I looked into the save file and:
Every Pokémon I've caught in this game is flagged. The error message states:
Again, these are all Pokémon I caught in the game during my playthrough, and have never edited or ported from another save. In fact, the Pokémon I've ported from my Scarlet save:
...are all fine!
So... what's going on, and how do I fix it? I took a look at the block data, comparing it to my Scarlet save. I spotted a few differences here and there, but nothing that would seem to indicate handler data. I'm thinking, in importing a bunch of Pokémon at the start of the game before receiving my starter, I may have inadvertently skipped some important flag or something, but I really can't tell. There doesn't appear to be much I can do in the OT/Misc menu, and even if I added my info into the Latest Handler slot, the error doesn't cease.
Any and all advice would be appreciated; while I'm a filthy hacker for giving myself money and Tera Shards, I haven't been hacking Pokémon directly or anything, so I'd like to know how to 'legitimise' this save file again.