Correct, it will still show the Avios for a new booking and a refund in your statement, but you don't need the surplus Avios in your account if you ring up, only the net amount. If you make the return booking yourself online and then phone up to link them then you *do* need the gross amount,
The only advantage of doing it yourself is that you don't have to hang around in the phone queue at a busy and inconvenient time. The disadvantage is that you can't get to the front of the midnight availability queue, so it's only really a strategy for rewards that don't disappear on the dot like SIN, SYD, MLE etc.