An early, if not the first, step in the REFRAD process is submitting a memorandum indicating your intentions. That is the document that needs to indicate that you want not only to resign your RA commission, but also that you don't want a reserve commission. Someone from the S1 shop/personnel office should have the memo template for you, and that template normally defaults to accepting the reserve commission. So, just make sure it's altered appropriately.
In theory, your S1 shop shouldn't let you submit the memo declining a reserve commission if you still owe IRR time, but if they don't catch it, then HRC should. The real test, and the answer for the OP, is your orders. Anyone undergoing REFRAD and therefore resigning his RA commission should have orders that say something along the lines of "you are reassigned to the U.S. Army transition point for transition processing. After processing, you are discharged from the component shown." And then, the orders should indicate that your component is regular Army.
If there is no additional language in the orders about reassignment to the reserve component, then that's it. You're done. Of course, if they mess up and accidently discharge you with an outstanding IRR obligation, I'm sure they'll find a way to recall you.