I am taking second opinion and then would move ahead with the appropriate treatment. Would prefer a biological dentist.
Good for you. The second opinion is the best thing you could do. The biological dentist is also.
Is filling these cavities by composite filing the best way, or should some other process be done?
Composite is what I have, but that was 15, or 16 years ago. There may be better options now. The biological dentist should be the one to ask.