Is doxy 100x2 30 days really a good regiment for very late syphilis? also can doxy cause a false negative treponemal test for very late syphilis?

Penicillin should always be used for syphilis when possible. Doxycycline is the main back-up when penicillin cannot be given, e.g. severe allergy. That dose is correct: just 2 weeks for primary, secondary, and early latent syphilis, 4 weeks for syphilis 1+ yr duration (or neuro-, oto- or ophthalmic syphilis). No treatment make treponemal tests negative; they remain positive for life.