@lfc20william You buy postage, not QR codes. You can use a QR code at the post office to have the postage label you bought on eBay printed there, rather than you printing it yourself.
With that cleared up, if you pay for two separate labels, you need to cancel one of them if you are not going to use it. Otherwise, eBay sees it sitting there as valid postage. In your case, if the QR code isn't scanned, it looks to eBay like you never shipped the item associated with it. eBay has no way to know that you put it in the box with the other item. This sets you up for a buyer to claim they never received their other order and there is nothing to disprove it, so you lose.
If a buyer does not buy their items together, you can still combine the order following the directions @bonanza125 gave you. If the buyer was charged separate shipping for each order, you can then decide if you want to refund them part of the overage. I personally don't do that, but some sellers do.
