I have had several pairs of vintage ebay purchases recrafted too. I don't guess any were seconds, so I can't speak to whether they will recraft seconds that you acquire from someone other than an AE store. I can't figure why they wouldn't recraft seconds from any other source, since you are paying them a lot of money for recrafting.
I read that some of the pre-worn AE's are stamped with a "W" on the bottom and AE will not recraft these. This may be incorrect, I have not tried to have such a pair recrafted.