Here's the thing: did they produce the total number of sets available, or only the number ordered? Either way, this is obviously a custom item, so for them to send you a replacement box, they are going to have to either print you up a new on on its own, or use one from an existing, already produced set, meaning the rest of the set has no box. And if they only produced the limited run, well, that's a set down the drain (granted, this thing ain't ever gonna sell out).
I don't know if companies produce extra sets for contingencies, but this set was touted as limited to what, 4000 copies?
I also highly doubt they'll just send you an entirely new boxset without asking for the other one back; that would be a dick move on their part to everyone else having issues.
What a mess all around.