I have some footage where I need to remove some light reflections that dance around over a subjects face. I remove them on a frame by frame basis using the clone tool but then when I play it back the corrections I've made are more intrusive than the original problem (a sort of smudge that dances around over the corrected area).
Your best bet is to try to composite the reflections out, or use other frames to clone from with Superclone. If the flare is not on frame 10 and a problem on frame 15, try to clone from 10 to 15. Or cut a hole around the flare with rotosplines, then slide a duplicate layer over to fill in the hole. Then feather the edges and color correct to match. Your last resort should be frame by frame cloning, since it will produce the inconsistencies you mentioned. If frame by frame cloning is your only solution, then I recommend putting on your favorite music, get comfrtable, and be patient, since every frame has to be perfect when played back at 24 or 30 fps. Remember that the viewer has never seen the original footage, so it is allright to change something as long as you keep it consistent throughout.
Fun stuff, huh? I just finished up three shots of a car with lens reflections dancing all over the place. Four of us have been busting our ass since Sunday to knock out about 600 frames in Commotion, After Effects, flint and smoke. Just delivered it to the client and they are very happy. I can see all kinds of problems, and wish I had another day or two, but as I said above the average viewer doesn't see the kinds of problems I see, and doesn;t know what to look for... this is the final test.