I appreciate your prompt response, @mcclin.

Allow me to chime into this conversation and provide you with some clarifications about deleting bills in QuickBooks Desktop.

In QuickBooks Desktop, only payments can be linked to an open bill. In your case, you'll need to delete the deposit that is showing on your transaction journal so it won't be recorded as money in the transaction.

Once done, you'll need to write a check and use the fix unapplied payments which can help to assign the unapplied payments to the proper bill.

To do that:

1. Click on Accounts at the top menu bar.
2. Select on Client Data Review.
3. Choose Fix Unapplied Vendors Payments and Credits.
4. The account selected should be Accounts Payable.
5. Select the vendor on the list. The Bills and Charges tab will display any unapplied payments and credits and open the bill for that specific vendor. 
6. On the Bill and Charges tab, put a check-mark next to the payment or credit on the left pane, and place a check-mark next to the associated open bill on the right pane to apply the payment.
7. If you would like to apply only part of the credit or payment, enter the partial amount in the Amt to Apply column.
8. Click the Apply button to assign the payments or credits selected on the left to the selected open bill on the right. The items are then grayed out to indicate that you have already assigned them.
9. Click Save to begin working on another customer record, or Save & Close to complete the task.

That should do it!

Please let me know how it goes by leaving a reply below. I want to ensure you're taken care of. Have a good one.