There are legislative means by which the federal government can recover funds. The recovery of funds is enshrined in federal legislation. The fact that it's a foundation does create a different situation, I think.
First of all, we have to determine who was ineligible. Then we can decide what measures to take.
You are right that there is an agreement, and that is a problem that the foundation should resolve. However, according to the agreement between the government and the foundation, if the foundation provided funds to a company that was ineligible, the government could recover those funds from the foundation. That mechanism still exists. The foundation will have to decide how to proceed with those businesses.