QB Issue Resolution:

Next time, use Pay Bills and look at the radio button for Assign Check #. That is how you use handwritten Bill Payment Check.

Entering the same details on a Write Check as are on the bill = duplicate. That might have affected your prior year tax reporting.

Resolution for Issue 'How do you show that you have paid bills with a physical check without deleting the bill from the system?' available: Yes (Solved).
Source: Intuit Community forum.

How do you show that you have paid bills with a physical check without deleting the bill from the system?: 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 Bill Payment Check
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Error Recovery for Bill Payment Check [Canada]
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