Lost DoD Security Clearance; Can I still get a DHS contract job?

I had a polygraph issue and some derogatory information came out, and now I am in the process of having my DoD clearance potentially revoked. I’ll still try to fight it, but knowing that it can take years, I started applying for other jobs. I was recently selected for a contract position under DHS that does not require a clearance, just a background check. Assuming I eventually lose my DoD clearance, will that come back to bite me in the behind at this new position?

Slightly separate question: does my re-adjudication stop when I am no longer employed under the DoD? What happens to the investigation?