When Starlight Glimmer prevented the first sonic rainboom from occuring, it prevents Applejack from coming back to her farm sooner. AJ left her family when she was a foal, by this time her parents are alive. A severely altered timeline could change the fate of these ponies.

In the Sombra timeline it's implied Granny Smith passed away. I can't imagine she would still have the will to live after what became of the farm. We also don't see Applebloom and I'm not sure where she could be but I doubt she would lose her life. 

We do see Big Mac and AJ working on their factory/farm but we don't see any trace of their parents. This implies Applejack has little to no correlation over her parents death if they're truly deceased. Or Bright Mac and Pear Butter are just somewhere else at the moment.

Another possibility is that Bright Mac and Pear Butter actually are alive, and they had taken Applebloom with them. No idea where they'd take AB but they'd probably wouldn't go as far as to force a child to do hard labor even in these hard times. 

It would be really dark if Pear Butter and Bright Mac are truly deceased in every timeline we saw and that they're destiny is to disappear no matter what changes. That or AJ and the first sonic rainboom have no effect of their fates.

Could the Apple parents Pear Butter and Bright Mac be destined to die or were they alive in a different timeline? In The Cutie Remark we don't see them...