Lyric discussion by SilverStarAlchemist 

Cover art for Are You Here lyrics by Corinne Bailey Rae

From what I can tell the repetition of "are you here" is her heart thinking out loud, in a sense.

A conflict exists between what her brain knows and her heart feels so she asks "Are you here?" because her heart is still filled with the same love she had for him before his departure.

For the heart, it's as if he never left. The brain, on the other hand, knows he's gone.