QB Issue Resolution:

open each one of the checks, one at a time, and change the account to Payables.

now go to Pay Bills, select the bills and apply the credits to the bills.

Resolution for Issue 'Cheques written instead of paying bills.' available: Yes (Solved).
Source: Intuit Community forum.

Cheques written instead of paying bills.: 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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