I'm now checked in - no shuffling occured as the flight isn't as light as I thought (still less than 50% loaded).
Question though: I can only download the Apple Wallet BP for the first leg (LHR-DOH QR2) but not the second (DOH-DAD QR994) - has anyone had that before? Is it due to a visa check...? [Seems odd to issue one BP if it is].
For the record: pressing the "add to wallet" button in the App just jumps to Wallet - I tried on mobile page in Safari and it seems it's only generating the one pass whichever one you actually try to save [I presume that they're normally linked so that you only actually save once for each flight series].