I would think the doctor prescribed an Antibiotic because they don't know what else to do. You say the biopsy was yeast negative but they found bacteria.. bacteria is in the mouth.. loads of it... so without reading to much into this I think the reason it started for you was the dryness + the lipstick acting as an irritant. Many toothpastes and hygiene products contain chemicals that (although pass as safe) will irritate skin trying to heal, and dry out the area as well. You wouldn't put toothpaste twice a day on a cut in your hand.. you would put a plaster 1) to lock in moisture 2) prevent abrasion while it's trying to heal 3) stop bacteria from getting in and infecting it. We can't do this for the lips.. they have to endure the erosion from that + eating + weather + stress.. really it is not wonder it takes so long to heal. ..as you have only had EC for a few months I would think the skin will heal back quickly provided you do not pick at them and keep them moist. Sadly you may have to go through the embarrasement of having this for a while...