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!

How do you handle customer overpayments? Customers pre pay for services yearly but we only invoice monthly, We use a two part system but the payments are in receivables. What is the best way to handle this? We have created a liability account called A/R before invoicing, however making the entry is making double entries happen. We still want the payment to reflect in the check register as when we received the whole payment to keep our check register accurate. Anyone have any suggestions?

Thanks for following this thread, smartin1124.

You’re correct in creating a liability for the prepayment. Since you’re using a two-part system, I suggest consulting an accountant for further assistance. They can recommend how to handle this type of situation. This also ensures your check register has an accurate record (whole payment).

Here’s a helpful reference that will guide you on how to provide a customer credit or refund. It’s scenario-based, so select the solution that suits your situation: Give your customer a credit or refund.

Additionally, this article contains resources on how to handle sales and other customer-related tasks. Make sure to choose the topic to view the complete information: Self-help guide.

Click the Reply button and post a comment if you have any additional questions. I’ll jump right back in to answer them for you. Have a good one.

Did you find a resolution for this? I'm having the exact same issue. 

I'll help you in resolving that, cglover123.

As mentioned above, the negative balance in your Accounts Receivable Aging Summary/Detail report represents the customer overpayments retained as available credits. To get rid of them, you can use the credit toward an invoice or refund the customer.

Feel free to follow these steps in giving a refund:

1. Go to the Banking menu, then choose Write Checks.
2. Choose the appropriate bank account.
3. Enter the appropriate check number and date.
4. In the Pay To The Order Of field, enter the customer that overpaid you.
5. Fill in the amount of the overpayment (credit balance) you wish to refund.
6. From the Expenses tab, click the Account drop-down menu and then choose Accounts Receivable.
7. Enter the same customer in the Customer:Job column.
8. Click Save & Close.

Once done, you'll have to apply the check refund to the overpayment credit so these two items won't appear as open: 

1. Go to the Customers menu.
2. Choose Receive Payments.
3. From the Received from drop-down menu, select the appropriate customer.
4. Click the Discounts and Credits icon.
5. From the Available Credits section, select the check you created and then hit Done.
6. If you see a prompt to confirm the transfer, just choose Yes.
7. Click Save & Close to complete the process.

If you want to apply the credit to an invoice, here's how to do it:

1. Go to the Customers menu.
2. Choose Receive Payments.
3. From the Received from drop-down menu, select the appropriate customer.
4. Tick the checkbox of the pending invoice, then click the Discounts and Credits icon.
5. From the Available Credits section, select the customer overpayment.
6. Click Done, then hit Save & Close.

Another thing that you can do is entering the overpayment as a tip. You may refer to this article to learn more about the process: Record an invoice overpayment as a tip. Take note that this is intended for QuickBooks Online. Although, you can use the same procedures for QuickBooks Desktop.

I also recommend checking our A/R Workflow Guide to learn the different ways of tracking customer transactions in QuickBooks Desktop.

Stay in touch with me if you need additional assistance in completing your other tasks. Have a safe and productive week ahead.

But does this change the income - all my negatuve transactions are just errors - we don't owe anything and I don't want the income to change.  How do I handle that aspect of it.  Calling QB is useless - can't get an answer.

Good evening, @Mary123042. 

Thanks for chiming in on this thread. Let me point you in the right direction to get this resolved. 

To be sure if this is the best route for you, I suggest consulting with your accountant. They'll be able to give you more details on how to fix this problem for your business. 

Keep us updated on how the conversation goes with your accountant. We're always here to have your back. Take care!