Yes, that's why the IRS extended to May 17. Once they do the calculation, your originally-owed amount will be included in the overpayment, and will be added to your new refund amount. So if originally you owe $1000 and now you have a refund of $500, your final refund would be $1500 (unless the IRS finds other errors etc.) you will get a letter in the mail about the adjustments made to your tax returns.
