QB Issue Resolution:

Create a check,to the vendor that your boss paid twice. And under the expense account I would select my  Accounts Payable account and enter the dollar amount that he paid. This would give you a credit to use for future and next month when another bill comes in from that same vendor you can use this credit to apply toward it the outstanding amount.

When the next bill arrives, enter it as usual. Then go under pay pill, select the bill and apply the credit that will be at the bottom of your screen.

Resolution for Issue 'My boss accidentally paid a bill twice. How do I record the money that came out of our bank account the second time? Until next month when I have a bill to apply it to?' available: Yes (Solved).
Source: Intuit Community forum.

My boss accidentally paid a bill twice. How do I record the money that came out of our bank account the second time? Until next month when I have a bill to apply it to?: 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.

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