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.
One idea could be that Rin, with her medical skills, tries to save Kakashi but fails due to some unforeseen circumstances. Maybe an enemy uses a powerful jutsu that she can't counter in time. This would be a tragic twist, as her being alive doesn't change the outcome for Kakashi.
A possible plot could be that Kakashi sacrifices himself to save Rin from a powerful enemy. This would be ironic as usually, Kakashi is the one protecting others. With Kakashi gone, Rin might then discover some secrets that Kakashi was keeping from her. These secrets could change her view of him and also drive the rest of the fanfiction as she tries to come to terms with his death and the new information.
No, Boruto is alive in the manga. The plot hasn't led to his death. However, the manga is ongoing, and anything could happen in the later developments.