In the sci-fi drama's third season finale, Peter (Joshua Jackson) was erased from history after traveling to a dystopian future world.
"The future that we saw in 2026 will now not have happened, because by altering the past, inevitably you set in motion a new chain of events that lead to a different future," Pinkner told TV Guide.
The executive producer also revealed that the fourth season of Fringe will include more glimpses into the past.
"There will definitely be [flashback] episodes, but the past would be different as well because Peter wasn't a part of it," he said.
Joshua Jackson recently hinted that Peter will be "a changed man" when he returns to Fringe, while co-star Jasika Nicole has promised that an upcoming episode will focus on her character Astrid.
The fourth season begins on Friday, September 23 at 9/8c on Fox.
> Castle actor Arye Gross lands Fringe role
Watch a video teaser for the fourth season of Fringe below: