Maybe AJ thinks her parents are dead, but they're actually trapped somewhere, like in some villains dungeon or turned to stone by a cockatrice.
You know it would be funny if they released new preview for that episode and showing things about current topic (like showing AJ parents and explanation of their absence). And that couldn't be mentioned here because of spoilers.
Because he know I'm going to go out in this plane and I'm going to remove one of His creations from His universe.
Watch the episode never bring any of this up.
Insert something witty that makes me better than all of you, here.
What would be funny is if they were just in the episode as if they'd been around the entire time with no explanation for why we've never seen them or why we'll never see them again.

AJ parents will overshadow AJ in this episdoe

Whatever as alive or deaed.
Because he know I'm going to go out in this plane and I'm going to remove one of His creations from His universe.
As much as I want Appleparents, they will probably never happen. If they were able to avoid Scootaloo's parents with such naturalness and ease, they can avoid AJ's.
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When All Else Fails, worry, that's the 14 way.

We will learn that AJ parents are dead, because they died just before this episode
Because he know I'm going to go out in this plane and I'm going to remove one of His creations from His universe.
@Death: Doubtful. But would be hilarious.
More
pluck than an Alabama banjo festival
I actually find the possibility of them never being mentioned at all quite likely, though that will only more or less confirm that they either deserted the family or are dead. Otherwise there'd be no reason for their absence to be not be the least bit noteworthy.
It would also be nice to see the Oranges from Manehattan again.
@Dave: That is perfect. XD
More
pluck than an Alabama banjo festival

AJ parents show up, and we see good explanation why we didnt was them before. And at end they die/abandon family
Because he know I'm going to go out in this plane and I'm going to remove one of His creations from His universe.
Applejack's parents are the Origami Killer!
You'd think the pegasi would just stop scheduling heavy rain after a while.
Life is simple: it has no nontrivial normal subgroups.
Just bought a whole boatload of Pony merchandise today in the rush before Christmas. A bit of it is for myself, other is for resale on eBay. Keeping for myself some trading card packs, a crystal pony and a Trading Card Collector's Tin with a bonus Twilight Sparkle foil card, a poster/cardlist and six fun packs, each containing 4 cards a tattoo sheet and a foil card or popup standee. (Same as the individual trading card packs.)
Is Babs an Apple or an Orange? I thought the Manhattan branch of the family was the oranges.