Checked-in today for 3 leg flight tomorrow within Canada. QR code indicated NA (or similar) for 1st 2 legs but for the 3rd leg. Scanned QR code successfully for 3rd leg. However, message have to check with agent for the 1st two boarding passes.

Go back in and now I can add QR code to second leg, but after five attempts gave up. In my thinking, you should be able to scan the QR code to your PNR once and allow the technology confirm it to multiple boarding passes.