Ian, my assumption is that you have the original clip in v1 and you added the lens flare as an effect in new clip in v2; this clip, in my assumption, has transparency in the areas where there is no flare effect. But Ian, this is just my guess, so if this is wrong what follows might not apply.
Suppose I guessed right. Then, you can apply the basic motion, keyframed, to clip in v2 to follow any path you want based on the motion in v1, and adjust opacity dynamically as well. If the issue is the application of keyframed basic motion to clip in v2, let me know, and I'll try to be more specific.
Piero