I have changed return times for New Zealand - Asia (usually China) - New Zealand on a number of occasions, using several airlines and often with a break in the return leg. The charge (so far) has been for the change in the return flight as a whole, not per leg.
I won't guarantee which of these I've done this on but I've travelled with Air NZ, QANTAS, Jet Star, Royal Air Brunei, China Southern Air.
You can book flights with quite different terms re change of time and, if you are certain that you will make a change, then it MAY be worth paying more initially if terms are better.
Offerings I have seen include (from memory)
NO changes allowed
One or two free changes
Up to N changes charged per time
Changes allowed charged per time.
Only within same far rules.
As desired of you pay the difference.
The airline can have two related fees and if there is an increase in far it will cost at least the difference. If the new fare is cheaper you MAY or may not get a refund of this difference.
Real world experiences:
I changed a Hong-Kong to Auckland NZ flight with Air NZ in December 2012.
Two fees applied in each case (I do not recall the rationale) and one was higher a few days later :-(. In one case they waived one but in the latter case applied both. A fare cost increase was also charged :-(.
On that occasion I felt "hard done by" by Air NZ BUT they have also been very accommodating in the past. On one occasion I (stupidly) got my dates wrong and tried to reschedule a Hong Kong departure next day and found instead that it has just departed (a day earlier than I had recorded). With some airlines that would be a lost international fare, no comebacks!. With AIr NZ they simply rescheduled top the day I desired and from memory there may have been no charge on that occasion!.
Lesson: Don't be a silly idiot ! :-)
QANTAS have also been very good:
I booked an NZ-China-Sydney + Sydney Brisbane + Sydney Auckland flight combination.
Meeting family in Brisbane for holiday after China business.
The airline (CSA?) messed things up horribly and I arrived about 15 hours late in Sydney.
I shivered the night in Sydney's ice-box airport waiting room (close to 0 C) and then attempted to reschedule my missed Sydney-Brisbane flight )(with QANTAS).
Bleary eyed traveller, sans luggage, rolls up to QANTAS counter:
"I missed ...
'I'm sorry sir, you have missed that flight, you'll have to buy a new fare.
"BUT it was xxx airlines fault that I missed the connecting flight.
'Yes Sir, we understand BUT as you booked the flights separately it's your concern if you miss the connection.
... Thinks ...
"OK. I understand. I have no right to expect not to have to pay BUT fortunately I'm dealing with QANTAS here and I just KNOW you are marvellous people who would not let a good customer down and that you'll find a way to get me a flight to Brisbane without having to pay QANTAS AGAIN.
... Discussion occurs amongst QANTAS staff.
They give me a 'free' flight! :-)
Asleep on my feet, I left my belt-bag in the Sydney XRay machine and arrived in Brisbane in the clothes I stood up in. The newspaper from my overnight attempt to stay alive still crackled under my shirt :-).
Lesson: Know what your fare rules say about missed connections!!!