There were several occasions when the structure of the timeline was nearly collapsing, and the world was about to be destroyed, but each time it was the Time Management Bureau who saved the day, anonymously bringing the situation back from the brink and allowing the world to continue as normal.
As for the Timekeeper, his ability was merely to stop time temporarily, not to traverse it, nor to directly affect the continuation of the timeline in any way.
Therefore, it naturally fell outside the jurisdiction of the Time Management Bureau.
The Time Management Bureau even went out of their way to belittle the Timekeeper's abilities in official documents, implying that such matters didn't warrant their intervention, when it was clearly the Superhero Association's incompetence at fault. Blaming them instead was downright disgusting.