I think you can convert them to xnb or keep them as png. both works in the game, the issue here is that the texture pack is out of date, and new textures that were implemented in the game later on, did not get updated in this pack.So, is the issue that all the Pokémon 3D\Content\Textures went to .XNB?
Cerrygrove.png ==> Cherrygrove.png?, and there are two modified .pngs i located, not sure whose is better or which is best to use.
Routes.png also has two modified .pngs i located, not sure whose is better or which is best to use.
Raistlin16 on 2013-09-13 and Dexter96 on 2014-08-17.
I'll upload all here, use Paint.net (freeware), layers are in XOR to show diffs.
That's what I think at least.