If the drones localize, you can get a constantly updating position over radio. Even with other tools, this will help disambiguate.

There are a few different parts here from robotics that can help.

  - Tracking allows you find a how a patch of pixels move. Look up "klt" and "SIFT features". Older
  - Recognition allows you to find a given object. Look up "yolo". Newer
  - Motion modeling allows you to predict where something should be, and can include the transponder ego data. Look up "kalman filter" 
  - All three of the above should be available in existing libraries
  - If possible, engineer the environment, like putting easy to spot LED patterns on the drones. This is always the easiest