Hi Mandy,

Let me show you how to deal with this in QuickBooks.

It is safe to create an invoice as it is the only way to clear the unbilled activities. Make sure that the invoice total will be zero. 

1. Go to Sales.
2. Click All Sales. 
3. Click on Filter drop-down button. 
4. Select Unbilled income on Type.
5. Click Apply.
6. Select the transaction you would like to create an invoice.
7. Click on Batch actions drop-down button and click Create invoices.