I had a customer order twice and I combined them together with intent to ship them both with flat usps rate. I refunded the customer the shipping overages. Went to mark it shipped with the tracking number and it wouldn't accept it. It cost me several percent.
@VinylAbundanceLLC : I think that there are two separate issues here. 1) You can combine multiple orders into a single shipment and use the same tracking number on both orders. We do it all the time. 2) If you are mailing your flats at non package First Class rates there is no tracking available. USPS does not offer it. If you are buying labels through Etsy, the number on the label is essentially a serial number not a valid tracking number. If I misunderstood your issue, please let us know.