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In my berserk playthrough, she still lives up until floor 7 ( the areana). But when I play as assassin, she was a pain to deal with. As assassin, you have the option to interact with her and help her with her questline. This is the same for Onyeka for berserker, Kaliska for sword artist and Azar for blood magi. They are not official party members like Hana, Bloodfang and Hachi( will join you in the arena event in floor 7), but you will team up with them in certain events.

is it good idea to let onyeka alive or kill her

When I challenge her alone she escapes and still lives but Hana was disappointed and swap hachi to her position

And then when I attack her as a team I killed her then Hana relationship increases 

What do you think?

Let her live? It will decrease the relationship of Hana

Or

Let her die? then Hana relationship will increases

(Please help me out I don't know what supposed to do)

That choice only effects the relationship aspect of the game I think.  Since none of the romance lines are complete, it really doesn't matter. If you let her live you will encounter her more. 

dont simp for the eldritch jail-bait