When Sisko had to explain the events of “Trials and Tribble-ations” (DS9 characters going back to the “Trouble with Tribbles” TOS episode) to the Department of Temporal Investigations, they asked him which of those types of temporal events he thought had occured. And the Defiant DID go back in time in that episode.

Also, the Voyager episode “Relativity” (Seven and Janeway time-traveling to prevent a bomb on Voyager) has the crew of the USS Relativity combining the different versions of a character that were created by the “temporal incursions” they had caused. In effect, time traveling in that episode created multiple timelines, and the Relativity was able to somehow combine different iterations of a person from separate timelines back together again.