QB Issue Resolution:

It depends on the tax you’re trying to pay.  Many states/agencies will only accept one payment for a payment period.  If you already made that payment, then you can’t make another one – at least not electronically.

In this case, probably contact the agency and ask them what to do. They may say to print and mail a check, or to include the amount with the next period’s payment.

Resolution for Issue 'Making Two NYS Tax Liability Payments' available: Yes (Solved).
Source: Intuit Community forum.

Making Two NYS Tax Liability Payments: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for NYS
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Error Recovery for NYS [Canada]
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