FBI Name Checks Hold Up Background Investigations

My position doesn’t require a top secret clearance only a public trust (non sensitive) but for some odd reason they discontinued my public trust and requested me for a top secret clearance. My supervisor requested they cancel it but I was told by the FSO that since they started it. They will process it. A incident happen 51/2 years ago and I’m afraid they may deny me . I made a poor judgement call. I was asked about it and I fully disclosed what I could remember and admited my mistake . If my top secret clearance is denied do agencies ever keep the employee and just downgrade the clearance. I do not access classified information.

Or do I have to challenge it in a hearing?