Thanks for following up with the Community, brookermans.
 

Now that you've ran your Audit Trail report, you can use the information on it to identify if these missing invoices were deleted. Also, the details displayed on this document can be used to recreate your transactions.
 

You'll be able to find steps for creating an invoice and applying a payment to it in Mark_R's post.
 

If there's anything else I can help with, I'm just a post away. Have an awesome Friday!