My Chimney has 2 flus ,one for the fireplace ,one for the oil burner?

,The mortar cap is deteriorated ,so I replaced a portion of it and sealed all the edges with mortar . The two flus are rectangular and rise perpendicular to each other and form a T at the top . Where the two flus meet at the top, there was a 1 inch gap between the two ,they didn't quite touch . I filled this gap with mortar but am not sure I should have ,but it seemed if I didn't it would let water get inside the chimney,where it didn't belong . I don't know if there was always a gap there or if some how they shifted apart. Do you think filling this gap is a mistake ,and why ,Thanks!!