I've recently been informed by our COR that apparently our contractor has been rotating personnel on our contract every few months after an employee receives their security clearance, allegedly so that the contractor can have a larger cohort of cleared personnel for use on other contracts and opportunities. The COR hasn't identified any performance issues with this, however his management has stated that it's costing our organization a significant amount of money to process all these clearances/investigations/screenings through DCSA. Does anyone have any experience with this kind of issue or have any suggestions on how to approach the problem?

Freyr, Some years ago, I wrote a contract clause declaring that the agency would pay for ___ employee clearances over the life of the contract, and that the contract price would be reduced by $_____ for each additional clearance above that number.

That's an interesting business model. Can't say I blame them if there is no oversight. Those things can get pricey. 

I believe @ji20874's advice above is the best. Tailor whatever your local security clause is to add. I would also add a notification requirement from the contractor  to the CO/COR to keep track of such occurrences.