QB Issue Resolution:

Thanks for the quick reply! If the payment that was created is a bill payment check, then, once a bill where it was applied to is deleted, the payment will serve as an available credit that you can use to pay another bill.

If you wish to re-enter the bill, you may just apply the credits coming from the bill payment check to pay it in full.

Here’s how,

Go to Vendors menu and select Pay Bills
Check the bill that needs to be paid and hit the Set Credits button
In the Discount and Credits screen, select the Credit that needs to be applied and hit Done.
Make sure that the date of the payment and the account to be used is correct before clicking the Pay Selected Bills

Resolution for Issue 'Payment has cleared but has no bill associated with it.' available: Yes (Solved).
Source: Intuit Community forum.

Payment has cleared but has no bill associated 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.

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