First, make sure you are not confusing the watch serial number with the movements COSC/Serial number. They are two different animals.
I have had TWO gen chronometers get out of sync in this area as the result of warranty service. If you read the fine print, the COSC cert follows the "original movement", but if you take it back a week later and the "Service Center" decides to swap the moment because they are too lazy to really fix it, you are now SOL when it comes to matching COSC paper work. This varies by manufacturer.
My guess, is the original owner had an issue/problem with the watch. Took it in for repair, and some sort of 'swap' occurred. The owner, now gun-shy about his high end Swiss timepiece, decides to bail out and sell. -or- as mentioned, the jeweler screwed up in haste.