She said that the infinity stones controlled the flow of time, and that removing one of them would disrupt the flow of time. But Thanos removed all six stones from existence, how come time is still flowing?
What I believe she was saying was that removing one would have drastic repercussions on the timeline from which it was removed. The Ancient One and her followers use the Time Stone to protect the Earth, and robbing them of it would leave the Earth vulnerable to mystical attacks. More than likely, moving forward from the events of Endgame Dr. Strange will have to deal with a similar situation in his own timeline.