That seems correct, since you claimed an excessive itemized deduction by deducting health insurance premiums that were already "deducted" from W-2 Box 1.
An amended return is an entirely different filing. Your original & amended returns together may still amount to a net refund. However, amending a return to add omitted income *or* (in your case) remove incorrect deductions is likely to result in additional tax due, even if less than your original refund.
