Sure, Kakashi is present in the Boruto manga. His role might not be as prominent as in the Naruto series, but he still has significant moments and interactions.
Kakashi is very much alive in the Boruto manga. The manga doesn't include his death. Maybe you got some misinformation or confused it with another character's fate. But for sure, Kakashi is around.
Perhaps there was some sort of dark influence or mind - control at play. An enemy might have manipulated Kakashi's mind in such a way that he believed Naruto was a threat and thus left him for dead, not realizing his true self.