I have entered into a civil agreement to pay back money embezzled and
have been makIng payments toward the debt for 14 months. The persons continues to threaten to press charges although I've been making payments on time and for te amount agreed. My question is whether charges can be made even though we've entered into a civil agreement?
Yes. Technically that person is not really in the position to decide whether charges will be filed or not - that person can only report what happened.
If you continue to make payments as agreed, it is highly unlikely any prosecutor would take the case given that the complainant is being made whole. If you quit making payments, then they could possibly file charges against you (assuming the statute of limitations has not run.)