Security Clearance Reprocity Applicability: Employee vs Contractor

BLUF: Is there a difference in applying security clearance reciprocity for the same agency as a federal employee vs federal contractor?

GIST: I was offered a position with a federal agency (Agency A), and I told the security specialist from beginning that I do have a current Tier 5 clearance. However, there was an unresolved incident report (IR). For some reason, the security specialist decided to order/request a new background investigation. Why didn’t the specialist request Research Recertify or Upgrade (RRU)? no idea.

Nonetheless, the unresolved IR was eventually favorably adjudicated. Later on, I was offered a position with a federal contractor to work on a contract with Agency A. Agency A’s security office accepted my previous clearance since it was within scope. Now, we are waiting for the date of indoctrination briefing with Agency A, which should be forthcoming in next few days.

I reached out to the security specialist and asked about the reciprocity. The specialist said that it would not be applicable because a new investigation was requested and JPAS showed “Loss of Jurisdiction”. After a little back and forth, I told the specialist that Agency A reciprocated my clearance and I am waiting for the indoctrination briefing date… but I have not heard back from her.

I don’t want to seem pushy or such, I wonder if there is a difference? I am trying to make sense of the process.

Feel free to share your thoughts or any advices/wisdom that you may have.