Flying birds photos

Sir,

While taking flying birds photos before sunset on the roof of my apartment, the auto focus gives away, and mostly I have to use manual focus. I am using 70-200 L series lens ( with or without 2x converter) and 100-400mm lens of canon with my Canon 5dm3.

Please guide me. I use Aperture priority mode with full permissible Aperture for lens. ISO is auto.