sounds like a long process but I would animate whatever scene your doing twice. first with a sphere blocking out the sun, then without it. track the sphere and add the tracking data to the null and delete the clip with the sphere. what youll be left with is a null that tracks the sun and you just do your thing with the flares
In the sky object's sun tab there's an option to use an object in place of the sun. I would place a null or light in there. If you're using a null, give it an external compositing tag and save out an aec file, with export 3D data checked. Before you do that, set the sun distance scale to something like 1%. Otherwise the null will be a million miles away.
If you use a light I think you can just export the aec with the lights option.
Then clear the sun>object tab and proceed as usual (but save the aec file under a different name if you're exporting other things).