If a character has the lorekeeper revelation...
lorekeeper:
Instead of encyclopedic knowledge, you learn most of your information through tales, songs, and poems. You may use your Charisma modifier instead of your Intelligence modifier on all Knowledge checks.
do knowledge skills count as charisma based checks for him?
Or do they still count as intelligence based even if he uses charisma for them?
They are charisma based. Whatever attribute you use to modify a check is the one it will be based on.