Happy new head canons for everybody!
This is a lot like my Spike and Celestia comic, it's an interesting idea, and although I don't believe it, I could see others doing so.
If the writers ever decide that they wanted Applejack's parents to be alive, this could be one way to do it.
It actually wouldn't be that hard to do, if the Wonderbolts are a branch of the Equestrian military, then AJ's parents wouldn't be around very much, (which could make a good episode, now that I think about it, sort of like a returning soldier thing and Applebloom is nervous about it).
They might not have been at the family reunion because they were needed elsewhere, which would be obvious to everyone so there'd be no need to mention them.
I say that if Twilight can have a brother that no one knew about, that is the Captain of the Royal Guard, then Applejack can have parents no one has seen that are Wonderbolts.
Some of you might say "Why did you pick those colors for AJ's parents? They aren't at all similar to the other Apples.". The reason I did so was because I based them on this painting on the wall (which is a parody of the painting American Gothic) at sweet apple acres [link]
. Also the similarities of colors between two ponies coats hasn't always been shown to represent familial connections.
Pony genetics... how do they work?!
If need be, you can imagine that Granny Smith's husband was a Pegasus, and one of Applejack's grandparents on the other side of the family was a pegasus, or that a great-great-uncle on the mother's side alone as a pegasus, according to Mr. cakes logic, or that it's a fan comic making a joke abot magical flying ponies and get over it
Also, the beginning is supposed to be slightly confusing.
Now if only someone could think up some names for them...
My Little Pony: Friendship is Magicİ and it Characters both belong to Hasbroİ.