I would hope (probably unlikely though) that they would have fixed that problem by now. But as long as you put the correct invoice # wherever that goes, on the return page, you will get the correct discount applied.
I went around and around with them, and that was for any non-RIM returns, about getting screwed out of the discounts. It was all over DFOAB and was happening to most but not all of us. It did turn out to be that if they couldn't trace it back to the exact purchase (by invoice #) then they would apply the largest discount you could have received on the part whether you did or did not receive that discount.
The problem was made worse by the fact that the field that needed to have that # was not a mandatory field (and I'm sure that was no mistake) so it was very easy to go right past it and screw yourself out of a bunch of money.
That fight with them brings back nightmares