Star Trek VI
ignored "Yesterday's Enterprise". Voyager's "Flashback" later tried to smooth things over by having Tuvok the events of STVI the "first
Klingon/Federation peace treaty"
Remember, the STVI writers originally planned to end the movie with a scene where Kirk and crew "hand over the keys" to the crew of The Next Generation
, oblivious to the fact that they're different Enterprises in different eras.