Maybe in the heat of the moment to protect his "niece", his fear of heights was overruled by his fear of a loved one getting hurt.

I'm gonna take a swing at this and guess that something happened between the events of Wolf Quest and those of Wings of Change that caused Boris to develop said fear. Obviously if that was the case, they never said what happened to cause it.

I believe they did this in Balto 3 to make the movie more interesting with Boris and Stella.

He also flew in WoC several times! The difference is that each time he flew, he was either close to the ground or had his eyes closed/covered. It's the same case in the first two movies, he was close to the ground when he flew.

Since he wasn't up high in the air, his phobia of heights isn't really taking a hold of him. I seriously doubt phobias of heights go into effect when your a few feet off the ground.

Plus, it was probably just something the producers threw in to add an internal conflict to the story and make it more interesting. Which could mean they either forgot or ignored the scene that Aiyana-Kopa mentioned.

Thank you, Aiyana-Kopa ^^" I forgot to mention that scene

He also flies in the first one in the beggining.
"I'm no spring penguin either. *starts flying* Oh its cold *shivers then falls*"