I'd say take the No.1 with them, it is the rider who won that number and it belongs to them for the next season to defend on whatever bike they end up on - but I get what you're saying about the bike
If VR didn't run with the No.46 and chose to use No.1 after winning his early championships then it would have been the case in '04 when he switched over to Yamaha from Honda after winning the '03 season with the No.1 plate on an unproven and fairly under-performing bike.