I actually called yesterday to try to work this out, because I bought an engraved iPad last week (arrived yesterday) -- I didn't use the edu store when I ordered though, even though I'm eligible, because there's no discount, so that apparently that made things harder for this...? He actually suggested I go to a store and return it 😕, which I thought was silly because 1) I don't want to give my iPad back just to wait another week for another engraved one, and 2) Why would Apple want my engraved one back? For most promotions like this (with other retailers) they extend back to whenever the return window starts (14 days?).
Anyways, he acted like he was doing me a huge favor by escalating it and seemed think it will go through in the end, but I'm surprised they don't have a more regular policy for this. I'm sure others experiences might be easier, but I guess you might have to do some convincing...