Yes that's right - they will redeposit your Tokyo leg Avios and immediately re-debit one half (to take account of the companion voucher); you will end up with an itinerary on one booking reference but the outbound and inbound will be different ticket numbers.

Thanks GCIFlyer. That is comforting. I thought that is how the general information read.

I love repositioning cruises but the associated flights are always challenging.