When your taxes got rejected, the payment to the IRS was rejected as well. Therefore, when you refile your taxes you should pay the full amount due, not just the difference.
If you only paid the difference, you can make an additional payment directly through the IRS Website here: https://www.irs.gov/payments.
You can check the payments listed for your IRS account by clicking here: https://www.irs.gov/payments/view-your-tax-account. Click on the "Create or View Your Account" link.