I sent duplicate invoices to a customer, and he paid on an invoice I deleted. not sure where the money went I don't see the payment anywhere.

I'll help you handle the deleted invoice where the payment is made, perfectionistplu.

Are you using QuickBooks Payments? While waiting your response, please know that we're unable to retrieve a deleted invoice. Thus, you can use the duplicate invoice with a similar amount. Manually mark it as paid to replace the deleted transaction. Here's how:

1. Go to Invoices.
2. Find the invoice.
3. Select the small arrow ▼ icon in the Action column.
4. Select Mark as paid.
    

You can browse this link if you need help with invoicing in QBSE: Tips about invoice and sending it your customers. 

Feel free to post any questions or concerns you have about invoices in the reply section below, and I'll be here to provide answers and assistance.