Hi Carving,
It's great to hear that you've been able to reconcile your account with the newly created invoice for your customer. Based on the information you've provided, t's my understanding that you just need to remove the previously recorded amount to clear it from your records. With QuickBooks Desktop, this can be accomplished in a few steps. Here's how:
1. Select Lists from the menu bar
2. Choose Item List
3. Click on the item you need to remove to highlight it
4. From the drop-down arrow beside 'item', hit Delete Item
Please note: If you delete an item by mistake, you must immediately go to the Edit menu and choose 'Undo Delete'. If you perform any other actions, you won't have the option to reverse it.
For future reference, here's an article to assist you with resolving common issues when applying a payment towards an invoice.
All the best!