If you are looking at the Tax Home web page where it shows your total refund, that is NOT an indication that the state taxes owed will be subtracted from the federal tax refund. That is only the NET you will receive between the refund and the taxes owed.
You will receive the full amount of the federal tax refund. You will have to pay the state taxes owed based on how you chose to pay those taxes in the File section of the program before the tax returns were filed.
