Think about this:
1) The Flash-Sideways has to somehow be important to the MTL, Darlton has continuously stressed that they would not waste the final season on "what-if" scenarios
2) Desmond is special and "the rules don't apply to him". He has moved through time and space like no one else.
3) He was on 815 in the Flash-Sideways and then disappeared
Widmore has brought Desmond to the island for a specific purpose; he knows about the electromagnetic pockets of energy and my guess is that he is aware of Desmond's uniqueness.
Desmond will reconcile the MTL and the Flash-Sideways. Maybe he will be able to move through both or he will go through another "Flashes Before Your Eyes" scenario. Either way, Desmond will be the answer to the mystery of the Flash-Sideways.
I will keep this brief so that others can speculate/elaborate on these thoughts; please leave comments in the section below.
Thanks for reading and enjoy the rest of Season 6.