I stand corrected about Henry's Blue/Green switches, it has been a while since I've read the book and it is still at my dad's house so I didn't have the chance to reference it.
I think the biggest thing I can suggest, is take the TV series with a grain of salt. Due to technical limitations early on, and then what I see as simply needing to institute further seasons to continue the show (and continue making money) they stray, and jump around alot. They can probably get away with this too, as most children probably only follow the show for a few years and then grow out of it, additionally at the ages they're following it they wouldn't always notice inconsistencies such as these. And the "purpose" of the show, much like Sesame Street or other childrens' shows geared at this age, is to teach life lessons such as cooperation, and that actions have consequences in a way children can understand, and it is hard to do this with a limited "cast" without repeating them to a point, if it has gone on this long. Just my opinion, I have never paid attention to the newer HiT stuff, so I could be wrong about that too.
Henry's forest was one of the first stories Britt had written specifically for the TV series and was never in the books, and was one of the stories that the Awdrys had the most issue with, not because it strayed from the books specifically, but because the Rev Awdry, despite having talking engines with faces, tried to keep things based on reality at every turn. In fact most of his stories were
based on things that had really happened at one time or another, either generics like cars breaking loose from trains, or very specific ones like a train falling down a mine or even a very well balanced turntable spinning like a top in the wind. He took issue with a line running through a forest, particularly with trees so close due to concern for sparks starting a fire.