So when do you expect the factory will provide you with the 2-layer design files so you can release them to all of us?
And did the factory really forget to tell you they had changed from the 4-layer board design you provided them to a 2-layer design for actual production? This would strike me as quite a remarkable thing.
The first inkling something had changed must have been the invoice in that case -- it must have been a pleasant surprise to see the price adjustment to reflect the significantly cheaper manufacturing process. 
And then of course there is the mystery of those RTC crystals just disappearing entirely from some production boards, but not others. I guess the factory must have much more discretion about such things than I would have guessed.
In the meantime we have the curious situation where a board is advertised as "open hardware source", and yet at this point in time no-one (including the original board designers) can get hold of the actual design files used for the actual production version(s). An interesting (but hopefully not long-lived) state of affairs.