I have Lyme disease. Tick bite when I was 10 years old, finally discovered I have Lyme at age 26, after years of suffering and getting more symptoms year after year. I'm now at the beginning of a long term antibiotics course. After 2 months of antibiotics, my foggy brain is starting to clear up again... for one or two hours a day in the evening I can think & focus again. The rest of the day I'm useless.
So it seems 2 months isn't enough to get rid of all the nasty bacteria, let alone two weeks! Yes, long term antibiotics has it risks but I wouldn't call it stupid when there's no other choice.
Furthermore, every 2 months the doctor switches the antibiotics, prescribes refrigerated probiotics with trillions of living cells & does regular blood checks (also for yeasts).