Unfortunately patched Pokemon games are not going to work with PokeTransporter. Your best bet is to:
1. Extract the save from the patched game with Checkpoint
2.Get PKHeX from projectpokemon.org and open your extracted save, which SHOULD be a .dat file if the game originated from a .gb.
3. All your monsters should show up in PKHeX, drag each one you want to be transported straight to your desktop.
4. Use Checkpoint to extract the save of the pokemon game that you want to transfer TO, and open that with PKHeX.
5. Now you can drag all of the pokemon you placed on your desktop to the boxes (Or your party) of the game you want to transfer TO.
This method should safely transfer all your pokemon over, good luck!