So I called up last night and managed to get through to somebody right at 11:55. I asked if it was possible to grab the return flight and add it to the first booking using another voucher. The agent put me on hold, and came back saying no problem, and gave me the price in Avios and taxes/fees that I expected. However, I would need the Avios refunded from my 2nd one way return booking in order to do this. She advised me that if I cancelled that booking, I might not get the Avios back immediately. With T-5 minutes to go, and already having confirmed seats for a departure day before, I saw the risks as the following:

1. I cancelled the booking in question, didn't get the Avios back immediately, and missed out on the new seats at midnight. The date I'd need to book for is the latest possible date that would work for my schedule, so I wouldn't be able to wait for the Avios to post back and try again a couple days later.
2. If I was able to get the Avios back immediately:
   1. The agent wasn't quick enough to grab the new seats at midnight, leaving me without a return.
   2. The original agent I spoke to was actually correct, and it would not be possible to add the return flights to my first booking - e.g. some type of error upon actually trying to ticket the booking and apply the voucher. I suppose in this case, I could have just re-booked a new one-way though as long as the seats were held.

The amount I paid for the one-way back to London was 5K Avios less than if I were using a voucher, but ~£380 more in taxes and fees due to the Avios & Cash combination I selected. In the heat of the moment, I figured a potential £380 net savings wasn't worth the risk of losing the seats completely, given how hard it's been to secure them (2 people business LHR-HND-LHR). £380 also felt like a reasonable cost to "pay" for a voucher, which I will still have to use on another booking.

Ironically, at midnight, I paid an extra £70 change fee to move to the next day's flight which has Club Suites, which I justified in my mind as a separate "upgrade fee" - not bad for 15 hours of Club Suites instead of the old J!

I've got some Seats.aero alerts set, so with significant luck, I'll be able to move to either JAL F / ANA J for either or both directions. In that case I'll just refund one or both of these anyway, and I suspect having them as separate bookings will make this easier to do if it's only a one-way cancellation / rebooking.

I've got to say, this has been the hardest booking that I've ever done but I'm pleased it's all set. It's been about 5 nights of staying up until midnight, trying to call at the exact right time to get through to someone, and trying to be very quick booking them myself (side note, I found that zooming out my browser helped give the edge of a couple seconds by reducing the need to scroll). Despite spending a bit more than I planned, I'll take this a successful outcome! Would be interested to hear any thoughts on my approach here or suggestions for the future.

Edited: Also, I think the way the booking was done was a bit of a failure of the original agent who made the outbound booking over the phone. I told him that I would want to call back later and add the 2nd voucher for 2 people, so it would have been great if he had done the outbound as 2 separate bookings with 2 PNRs, in which case the change may have been easier. Oh well, you win some, you lose some, and I'll still take this as a win!