Not sure if you've resolved it, but I was researching the same issue.  If you created the bill as a bill payement due, then paid the bill outside of QB online, meaning you did not use the pay bills function, instead went to your bank bill pay or direct to the vendor site, QB does not know you did that.  You can go back to the pay bills icon, click on a bill which will allow you to edit it. Then, at the bottom, click the more button and select delete. The "accounts payable" that was there should not be gone.