I watched the part of the movie where The Ancient One and Hulk/Bruce Banner talk on Youtube (here) a few times. The Ancient One doesn't say that by bringing the stones back to the right moment the emerged timelines will disappear, but it's Bruce Banner who suspects it and and convinces The Ancient one with this idea. Whether it really is the case that the alternative timelines are disappear by bringing back the stones is not said and in the comics it's not the case that the timelines disappear again. The Soul Stone is also brought back, but without undo the death of Black Widow.