QB Issue Resolution:

Bill Pay within QuickBooks Online is now available through our partnership will Bill.com.  You can now pay vendors directly using ACH or have paper checks mailed for you, directly inside of QuickBooks.

To learn more, just visit this link: https://community.intuit.com/browse/quickbooks-online-apps-billpay.

Resolution for Issue 'Does QB Online have any capabilities to pay Vendor Bills using ACH payments. We currently use Bill.com but are unhappy with the inability to sync credits.' available: Yes (Solved).
Source: Intuit Community forum.

Does QB Online have any capabilities to pay Vendor Bills using ACH payments. We currently use Bill.com but are unhappy with the inability to sync credits.: 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 ACH payments
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Error Recovery for ACH payments [Canada]
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