We’ve had this situation before and seats were allocated at the airport.
Some seats will be occupied by pax flying only SYD-SIN. Others will be occupied by pax only flying the SIN-LHR sector.
Then there are the pax flying SYD-LHR, effectively a third seat plan within the same flight.
We flew on our booked flight, sat together, but in different seats on the two sectors. It’s the two different seats on two sectors with the same flight number that the IT couldn’t deal with and had to be dealt with manually.