Would not affect the test.
The tests look for the immune system's response to the bacteria, not the bacteria themselves. Eight weeks after putative infection, the immune system would be active, and the antibodies would be detectable. If the drug killed the bacteria two days prior to the test, the immune system would still be on high alert, and both trep and non-trep would be positive. It takes a while (months) for the non-treponemal response to go down after successful treatment, and the treponemal response may never go down.
Also forgot to mention that the test would done 8 weeks post exposure.
The tests turned out negative today. I'm relieved. It's time to move on with my life.