Looks like MO will take your refund and use it to reduce the balance due on your payment plan.
Refunds, credits, or debt offset payments to an account will not be considered an IIA payment. However, this will reduce the balance due on an account. https://dors.mo.gov/DOR/CACSGIIA/IIA/pdIIAPersonalTax.jsp
**Answers are correct to the best of my ability but do not constitute tax or legal advice.
