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1. Use Hopeless Trainer Editor by Esperance instead,
2. Go to its ROMs folder and edit the corresponding .ini file,. If you use Firered English, edit the BPRE .ini using notepad.
3. When you open the .ini file using notepad, you will see Count=412
4. Simply change the 412 to the total number of pokemon you have in your ROM. Then save it.
5. Open HTE execute file, it should read your expanded pokemons.