I left right in the middle of an email conversation with them, so don't know what the end result turned out to be. They offered to reprint the whole job and our position was "Nah, you did a bang-up job otherwise and this is a tiny error on a complicated layout. Just really hook us up with a good discount on the next thing we order."
I expect to be using them quite a bit in the future, and though the error was theirs and not ours, I don't want to start off as the customer for whom they had to eat 576 t-shirts for one missing character out of thousands.
I'm still not convinced they re-typeset the whole thing. I think they probably used our artwork for the first 40 because they thought that was all that would fit, then later manually added back in the last 6 when they realized they'd fit.
Anyway, it was a relatively minor flaw in an otherwise really nice job. Overall, I'm really tickled with these shirts and they came out much as I'd hoped.
We won't be in as much of a hurry on future jobs so I'll be getting proofs in the future.