The Flash fans may remember that the device was powered by the multiversal particles of all living Wells, so it stands to reason they escaped when Barry damaged it.
This would mean the original Harrison Wells is alive and possibly living with the knowledge of all other Wells.
It seems that the Harrison Wells resurrection took place in the present, sometime shortly after Barry destroyed the artificial Speed Force after his speed thoughts ruined everything.
Much like with Nash Wells, they need an organism to exist in, and they just so happened to find the perfect one lying in an unmarked grave.