Pokémon Yellow editing issues (Maybe R/B too)

[PokeMintspree]

After sending Pokémon from my Crystal VC save to my Yellow VC save back and forth, it seems only the PC box I had last chosen on Yellow has Pokémon in it but all others are empty. PikaSav and PKHeX still shows the Pokémon are there too, the only workaround currently is using PHBankGB to store all my Pokémon before making edits… but I have read this is apparently a fault of RBY and not PKHeX, but I already was 4 gyms into the game and using a few of my boxes? It sounded like it only happened if you tried editing boxes before you changed a PC box for the first time. Does anyone have a solution to this?

[Maetch]

This happened to me in Red, too. I thankfully had a backup to undo it with, but this may be a problem later on when I go for the full Pokedex.