Reginald always intended for the children to be used in the machine, but Ben's death, five's disappearance, and Viktor's instability meant he could not complete his mission in the original timeline, so he goosed things to cause the Umbrella's to break the timeline and become a more effective team, however Harlan killed his original intended subjects, so he tried again with the Sparrows; having completed his grand plan, he restored the Umbrella's to the timeline, sans powers so they could not try to reverse his actions at some later point. The Sparrows never existed in this new timeline, though the appearance of another Ben could mean they all have Doppelgangers and there is another version of the Sparrows out there.
Season four should be interesting.
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Why didn't you DODGE‽‽‽ Quoting me will trigger the profanity filter, Not Joking. I've been Scunthorped! Consider yourself warned.