It is simple. Do not apply for a new medical until the issue is cleared up and a AME that knows what they are doing thinks you are ready to fly. That way when you fill out the medical application, you do not get a denial from the application, will put the incident down on you visits to the doctor and go on from there.
Unless there is a major issue, I would just not fly until the problem get better. If you need a steroid injection get the approval, but do not fly on it. Once the back issue is fixed reapply for a medical and return to work.