I'll try to do a Game Sync after the injection. I'm screwed anyway...
If succeed, I'll post the result here for the future. Just enjoying the bad happening to do some experiments.
For example, I noticed that if I create the Pokémon in an edited save and use the Bank, I can transfer without any problems to another save that I use for Game Sync. That's because PGL checks some flags for each Pokémon. If it exists from nothing, without an entry for capture, trade, transfer from Bank or breed, it will be marked as hacking
So, I think that my problem started here