Hi Freddy21,
That sounds like a hassle. Allocating a customer payment shouldn’t remove freight from a recorded invoice, so I’d first open one of the affected invoices and check whether the freight is still included in the invoice total and Balance Due before sending the statements.
If the freight is missing from the invoice itself, go to Setup > Linked Accounts > Sales Accounts and make sure “I charge freight on sales” is selected and linked to the correct income account. Save the change, then test it with a new invoice. If the invoice total still includes the freight but it only appears to be missing on the payment allocation screen, please share a screenshot or support case number so the specific transaction can be checked.
For more information, please check this help page for detailed guidance: Managing linked accounts.
Regards,
Earl