When you begin the amending process, you will notice that your estimated refund amount drops down to $0. This does not mean that you are no longer eligible for the refund you were to have initially received from the IRS. This is to help estimate how much more your may be eligible to receive, or how much you may be required to pay - in addition to the refund you have already received.
You should still receive your refund from the IRS. If you see a negative amount, you will need to pay that amount to the IRS after you have received your refund.
However, it is recommended that you wait until after you have received your refund from the IRS to begin the amendment process. This is because the IRS may make changes to your return to more accurately reflect your tax situation.