Transferring contractor TS to Federal Service Secret with red flags

I am currently a DoD contractor with a TS SCI clearance. I currently have an opportunity for federal service with another agency. The position requires a secret.

I ran into some issues with my current contract - while I still maintain a TS SCI, I ended up in a different position on the contract because I was denied a SAP. The reason was due to my girlfriend who is a permanent resident from China. This information is on my SF-86 and I was still adjudicated favorably for top secret during my last investigation.

Will I run into to any problems with this trying to enter federal service? The clearance required is only a secret and everything has been reported on my SF-86. This is a completely different agency from DoD. It is not IC, DHS or DOS.

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