these two threads are linked aren't they?
Anyhow if the PID is stored, we can make convincing recreations. Most Pokémon commonly use Method 1 for PIDIV generation (and encounter slot information can be derived from that, to cross reference against met location data), so it won't be an issue. Give us the save and we can check that.
Also, there's a chance the mon you extracted wasn't saved was either not saved as pk3, or you weren't using PKHeX with a Gen 3 save loaded.
Poketransfer isn't a location in Gen 3, and if PKHeX showed that, either one of those things were likely wrong.