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I will look at HMA when next I am able to sit down and work on this. I am putting in the index correctly. I have used two different trainer editors and they all show that it is the correct pokemon. The pokemon in question can appear in the wild just fine. This only happens with trainers' teams...
I have been using Hopeless Trainer Editor and in both that and the trainer editor in PGE the pokemon look correct. In actual play they are getting replaced with pokemon that have a similar index. Roxanne's Nosepass becomes a Kadabra, Brendan's Marhstomp becomes a Sandslash. Things like that. In...