I have an active secret (DOD). Recently, I am in my native country and I used foreign passport unknowingly that it could raise an issue. After while, the company told me that I SHOULD NOT USE ANY FORIEGN PASSPORT, and I might get CI screened again or even worse not get screened and unable to go overseas for the job !!!
I did not know until they told me that even entering any country is not allowed with foreign passport, but I was reading that " A foreign passport is permissible for entering or exiting foreign countries – theoretically even third-party countries that the clearance-holder could enter or exit on either passport – but it can never be presented at a U.S. border crossing ".
So, when I left US I handed my US passport and foreign passport to airline agent, so I do not know how could that affect my clearance?