It seems to have been an accidental consequence of whatever Nick and Helen did together back in the Permian, since they returned from there to the altered timeline.
One of them must have stepped on a butterfly.
The thing that's confusing to me is that since that first series ended with the new universe there hasn't been anything similar when IMO they've done more significant 'changes' to the past in season 2 & beyond than they did in S1. In Season 1 they always made attempts to get the creatures back into the past and not disturb things. Once you added more military components as the show went along more creatures were killed and not returned to the past.
Then you finally get to the biggest change to the past in the show's entire run. You had Connor & Abbey spend an entire year in the past killing fishies, stepping on bugs, etc... and they come back to an unaltered future? Obviously the arc has gone through changes, but that can be explained by it being the same timeline and just new management.