When you void a Bill.com payment, the change will not automatically sync to QuickBooks Desktop. You will have to update it manually. Therefore, after you void a payment in Bill.com, go in and manually void the matching payment in QuickBooks Desktop.
Please see Quickbooks desktop help article Quickbooks Void Payments for more information.
When you void a payment in QuickBooks Desktop, the amount of the original payment changes to zero as of the date of the payment (there will be a $0.00 in the clearing account) and the word "Void" is added to the memo field on the payment.
When we process the Bill.com credit, a journal entry syncs to the clearing account for the credit to balance out the original payment Funds Transfer entry.