We have a similar situation. My wife and I are going to New Zealand in November with a few days in Singapore en route. Our travel agent booked us flights with Air New Zealand, operated under a codeshare by Singapore Airlines. I’m trying to book seats, as we want two together, one of which has a window, but it seems impossible online.
The Air NZ website says that it has to be done via the Singapore Airlines website, but that says “Specific seat selection is not available on this flight, as it’s operated by our partner airline. Please choose your preferred seat type, and we’ll do our best to ensure that our partner airline fulfils your selection.” So we have a situation whre ANZ says we have to talk to Singapore, but Singapore say they can't do it because it's operated by ANZ!
Somehow we’ve managed to get a window for my wife, but the only other options available are aisle seats – so we can’t sit together. I phoned both airlines some time ago, as my wife needs a special meal, and the person at Singapore said she’d arrange for us to sit together. So far there is no sign of this having been done. Do we simply have to hope that a pair of seats with a window will be available when we check in? It seems fairly unlikely, even if an A380 has more windows than most aircraft.
We'd be grateful for any advice.