QB Issue Resolution:

Don’t mess with the completed transaction.  Just pay the customer and use your refunds income account as the expense for the payment

Resolution for Issue 'On a single invoice I charged for four different services at $500/each that were to occur over several months. The customer later decided they didn’t want two of the services. The original invoice of $2000 was paid in full. I need to refund $1000 for only those two cancelled. When I try to process a refund I receive the error message “CustomerX’s payment doesn’t have an open invoice to go with it”.' available: Yes (Solved).
Source: Intuit Community forum.

On a single invoice I charged for four different services at $500/each that were to occur over several months. The customer later decided they didn’t want two of the services. The original invoice of $2000 was paid in full. I need to refund $1000 for only those two cancelled. When I try to process a refund I receive the error message “CustomerX’s payment doesn’t have an open invoice to go with it”.: 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 create a partial refund
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Error Recovery for create a partial refund [Canada]
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