Standard CX phantom availability or something weirder?
 

I'm trying to change my BOM-HKG Avios booking in J on 25/10 to 28/10. Availability shows fine on BA.com and awardnexus. the call centre agent said he can see it too but its availability is showing as 'waitlisted' status rather than the typical 'confirmed', which according to him is as good as not available.

Is this the standard case of phantom availability, and if so I assume there's nothing I can do?

I've never heard of BA showing space that is waitlisted. If you have the Avios try making a separate booking for the 28th and then cancel your original booking. The fee is the same for date changes and cancellations. I cross checked on both BA and Qantas and see Business available on both BOM-HKG flights on the 28th. So it's unlikely to be phantom space.

Actually there's more to this story, which might be worth knowing...

Currently I'm booked on CX660 BOM-HKG 25/10 connecting to JL026 HKG-HND.
I'm trying to change to CX660 on 28/10 connecting to CX548 on 29/10. Availability for both is OK on BA.com.

I just spoke to someone else and we tried this:
1.) Search for BOM-HKG and HKG-HND separately, which shows availability ready to book.
2.) But when you add the BOM-HKG into the booking on the new date then the HKG-HND availability disappears
3.) If instead you add HKG-HND first then the BOM-HKG still shows up but as 'waitlisted'

Is there any logic to this, and any way to get what I want?!

Unfortunately I don't have the avios at the moment to book this as you suggest :(

To me, this sounds rather like a married sector availability problem rather than simply phantom availability: There isn't one single answer to whether there is availability on a specific flight, because availability depends on your overall itinerary.

Applied to your case, it may be that CX will make a seat available to you on BOM-HKG if your itinerary is BOM-HKG, but not if your itinerary is BOM-HKG-HND; and likewise there will be availability on HKG-HND if your itinerary is HKG-HND, but not if your itinerary is BOM-HKG-HND.

One way around this may be just to book separate tickets for BOM-HKG and HKG-HND. As you're stopping in HKG for almost 24 hours, this may be less problematic than for a shorter connection.

Good point, seems like married segments always get in the way of what I want to do so I should have thought of that first!

Have you tried HKG-NRT? Or even HKG-KIX? Maybe that might not have the same issues.

NRT works but I'd really prefer HND because I'll be taking a domestic flight a few days later and I have awkward luggage that I'd prefer to store at the airport. I know the luggage transfer services are good but I can't find clear size restriction so I don't want to bank on it.

This is a very typical married-segment problem.
Even AM members have it. Even paid pax. BOM-HND is quite cheap compared to HKG-HND and CX restricts availability on HKG-HND for BOM originating pax.