I think we'll find that because the outbound is being changed, the whole itinerary is being repriced at today's rates, but using the return segment as currently booked (and has been booked for x days/weeks/months) meaning the lower fares won't quote, as they would need to be ticketed within so many hours of the booking being made.
On your next call OP, either ask the agent to cancel and rebook your return from availability, or switch your return to another flight/date/gateway and see what happens...
It seems to make sense to not touch the return that isn't changing, but that's probably what's not helping here. If return availability was an issue then leaving it alone would probably be best, but since lower fares are still selling, letting the space go and rebooking might just work.