I'm sorry to bother you again. This will be my final clarification. 

Contrary to Dr. Handsfield's advice, I took the full 14 day 100 mg Doxycycline.(no dairy or alcohol) and i took it with food. 

In the first 4 days every symptom disappeared and I forgot about this whole thing by the end of taking the medicine. 2 weeks after the last dose( 9,5 weeks post exposure( my neck and groin lymph nodes became painful), and in the upcoming days the same maculopapular rash on chest appeared and is on whole torso now. Its most prominent in the morning. I retested with TPHA at 10 weeks - result pending, and INSTI rapid treponemal test is negative at 10.5 weeks. 

1. Could it be that doxy did not work, and it messed up the seroconversion process? 

2. When to retest after antibiotics to be sure? 

Thank You! 

The doxycycline you took, as Dr. Handsfield told you, is highly effective for syphilis treatment and, if you had syphilis, would have  cured it.  You do not, and did not, have syphilis as your blood tests show.  If your symptoms had been due to syphilis, the tests would have been positive despite the doxycycline that you took unnecessarily.

1.  If the doxycycline had not worked, your test would have been positive.  Further testing is not needed and if you choose to not take the advice provided on the Forum, no matter how much you test, the tests will show that you did not acquire syphilis.  The symptoms you describe could have been due to any of the numerous community acquired non-STI viral illnesses that most people get from time to time.  

2.  See above- no need to retest.

Further, let me remind you that falsely positive tests do occur from time to time and the more you test, the more you are to have a falsely positive test.  EWH