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This is probably the most exciting hack I've seen in a while, mainly due to the fact that I've always been a bigger Digimon fan and it looks awesome.
Just looking at what you have done and knowing what's left to do I can see this will be hard work and for that you have my up most respect and...
To me (and I'm no expert) it sounds like a problem caused by not having a National Pokedex, it will cause and poke that isn't in the Fire Red dex to not evolve. But like I said I'm no expert and I haven't started this hack yet, I was just about to hence why I'm checking the thread.