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If the project IS invoiced at the project level the invoice can be created anytime
Periodic Billing
Periodic billing is used for customers that are paying for multiple reports all on the same invoice - like Projects that are invoiced at the report level
Select the customer > view all reports ready for invoicing that have not yet been invoiced
Review then create the multi-line invoice - one line for each report
Invoices will be visible from the report and the project, project discounts will be applied