For cloned bookings, you may prefer to create separate invoices.
1. In Settings-> Organisation Configuration, under Invoice & Xero Configuration, select Generate Separated Invoice for Cloned Bookings box.
2. Click on Save button.
3. After enabling the option in Organisation Configuration, , separate invoices will be generated when you clone a booking.
4. In booking page, click on Finance -> Download PDF Invoice option to have access to invoices in one PDF file.
5. You also have access to separate PDF files of the invoices in Finances-> Guest Invoices and you can send them separately to the guest.