Okay, wait, wait, wait. If the grandfather paradox is destroying all the timelines, even the Commission, then the only timeline that would be left is the one Reggie makes after Hotel Oblivion. Then what are all the timelines the subway is connected to? How did they survive the kugelblitz?
Possible theory: the Commission is wrong about how many timelines there are, and there are timelines beyond their reach that also aren't destroyed by the kugelblitz. But if so, then the Cleanse shouldn't affect them either.
So, I conclude there are timelines that are not destroyed by the Cleanse in season 4 (which is my headcanon).
Or else someone at the studio did not hire a time travel consultant.
P.S. To make matters even more confusing, Herb distinctly says "the timeline is collapsing," which implies only a single timeline. Yet if another Five founded the Commission, clearly there's more than one. I request a five-minute interview with Founder Five just to get this all sorted out.