Russiangeneva,
Have the customs folks been able to help you?
Also, have you spoken with the BVet? (
http://www.bvet.admin.ch/kontakt/index.html?lang=de )
The strict importation rules are in place to prevent Swiss residents from going outside Switzerland to acquire a docked dog as a get-around. However, the
primary goal of the ban on docking and cropping is animal welfare; while I have no experience of your situation, I would think that forcing a family to abandon a beloved pet because of a clerical error would not be something they would insist upon. My experience has been that the BVet are reasonable folks.
Can you show proof that your dog has been a family member for quite some time before the move? Can you show them why - leaning heavily on animal welfare reasons

- you were unable to bring him to Switzerland with you when the family first moved?
I would think - bearing in mind that this is only my opinion - that if you approach BVet with a reasoned argument they would be willing to help you.
Another possibility would be to contact a professional animal shipper. These folks generally are very well versed in the rules and regs of getting animals across borders, often well-connected, and might have be able to help you. One such firm here in Switzerland with a good reputation is Ace Pet Moving. (
http://www.acepetmoving.com/en/about-us.html )
Also, you might want to post a question in the Pets section; there are folks who have brought in docked family pets whose experiences might be relevant; perhaps they might not have seen your question in this section.
And, may I ask that you post an update when you find a solution? This info might be valuable for others.
Hope it gets resolved quickly, and that your pup is soon running in the Swiss Alpine meadows with the family.