There's the moment where Henry is let out of the tunnel after The Fat Controller asks him to pull the heavy express.
In the ending, Edward and Henry take Gordon back to the sheds, thus cementing the three's friendship.
Main Line Engines
In "Buzz, Buzz", Duck's dislike for diesels was remedied after BoCo came to the sheds and revealed that he was a friend of Edward.
Edward, who's often mocked for being the oldest engine, uses everything in him to pull a train after a serious breakdown. He shows up late at the station, but the passengers are so proud of him that they give him a round of applause.
There's also Donald and Douglas being the last of the engines to accept BoCo into the family.
James and the Diesel Engines
In "Deep Freeze", James becomes more accepting of diesels after one of them had helped him after his injector fails.
More About Thomas the Tank Engine
In the ending of "Drip Tank", there's Thomas apologizing to Percy for his behavior towards him throughout the start of the book, especially when calling him a drip. Even more heartwarming when he asks that both of them can be friends again, which makes Percy happy.