Transfering Pkm files from another save in PokeGen gives a Full Pokedex...is this normal?

[PkmnTrainerAbram]

The target file the Pokemon were transfered to had 170 Pokemon seen. Game was Pokemon Heartgold USA.

The file the Pokemon that were transfered FROM had 492 Pokemon seen and caught. It was a Living Dex file I worked on back in 2012, Pokemon Heartgold Japanese ver.

I merely wanted to mass transfer files from one save file to another using PokeGen, to avoid transfering wirelessly. I expected that by doing so, that the Pokemon would not be recognized in the Dex, but the exact opposite extreme happened.

Is this...normal when transfering Pokemon files from one game to another? What possibly could have triggered this? I had a backup of the file luckily, and even if this is normal and has no ill effects, this isn't how I wanted to complete the dex on that file.