Two investigations: what are my options?

Hi, I would greatly appreciate an insight on what my options are at this point. I was favorably adjudicated l in March/April of 2022. A federal contractor sponsored me to work for the agency in MD. I was awaiting for the contractor to file for the agency access. While I was waiting I applied to two positions with the agency directly and passed and was conditionally offered both. the Agency began a new investigation regardless of my favorable adjudication. Another SF86 (but my family and friends weren’t contacted), met with an investigator for two straight days. Then it was the time for poly. I didn’t pass the first, passed counterintelligence questions during my second, but had inconclusive results for “foreign intelligence contacts”. I passed the third poly, and the examinator said that “you passed, but I didn’t get to ask you all the questions. Now an adjudicator will decide if you need another polygraph”. In a week it will have been a month since my last poly so I think that I may hear something on what’s going on. Meanwhile, the federal contractor keep pressuring me if I am still interested in the job with them. Here, as I understand, I have to file for local agency MD access and that’s the end of the journey (I received an email with the link). If I am favorably adjudicated by the agency, I really want one of the positions because it is similar to what I am doing now as a federal employee without TS/SCI and love doing it. However, I wouldn’t mind working in the other capacity (the position currently offered by the contractor). If I am not favorably adjudicated by the agency for the second investigation done second time in a row for the same place, could I still use my TS/SCI and gain access to the agency? I heard various opinions. Some say if it is a no, it is a no. Another stupid question, if it is the same place, why was I investigated second time after I was already favorably adjudicated?