general problems of the 2013 Mazda MAZDA3

I have a 2013 Mazda 3i 5-door hatchback with approximately 61,000 miles, 90% highway driving to and from work. After having the battery replaced (original) earlier this year, I then noticed that my headlights would flash intermittently, at that time. As the year progressed, the headlight flashing, which presents itself only upon braking or deceleration, became markedly increased and brighter, including the dashboard information systems window inside. I went to an authorized mechanic, who first put my car on diagnostic, which showed that the alternator was very weak/worn. Since I had extended warranty, through a private company, but only until 60,000/5 years, I rushed to make time for the mechanic to receive authorization and replace the alternator, which he did, and my car runs great. There remains, though, the problem with the headlights flashing. Since the mechanic did reset the computer, we were stumped. Then my husband found a service bulletin from Mazda dealing with this specific issue, stating that the car must go to the dealer because only the dealer can reset all the parts of the computer. I then contacted Mazda, but have yet to receive a response. I do not feel that I should be made to pay for this adjustment/repair since Mazda apparently is well aware of this problem with this model car. Just google it, there are alot of m3 owners out there with similar problems, most got resolved because they were still under warranty. Great for them, but that doesn't help me. Not only is this a problem for me since I drive nearly 40 miles each way to/from work each night, but I am tired of other drivers flashing their lights at me, honking, or yelling. It is most annoying, not to mention a safety hazard, since I am a night-time/early morning driver, predominantly driving in the dark. Please advise.