Travel with a schengen visa from on country to another

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My wife ( Vietnamese ) and I took a flight from Frankfurt on the 17th June, flight SK1636 to Copenhagen, we had a return flight booked from Copenhagen to Frankfurt via Zurich LX4665 and LX3610 to Frankfurt. On arrival at the check in desk at Copenhagen I requested my luggage to be sent direct to Frankfurt, this was done, but when I asked for our tickets to also be direct to Frankfurt I was told it was not possible and I would have to go to the transit desk in Zurich to collect our ongoing boarding pass, I asked again to be ticketed straight through as my wife has a schengen visa and we should be ticketed straight through, again I was refused, when I asked yet again, I was very rudely told that it could not be done and we had to go to Zurich. On passing through passport control I explained to the officer that we were going to Frankfurt via Zurich, but because our boarding pass only showed Zurich the officer cancelled my wife's schengen visa, on arrival in Zurich, where incidentally the flight was over an hour late so we had missed the connecting flight anyway, my wife was then told that she had to go back to Copenhagen as she no longer had a visa for Germany and as I have an EU passport I was informed that I would have to purchace a return ticket to Copenhagen, as there were no flights available to take us back to Copenhagen, what this would have achieved I don't know as my wife now had no visa. Our only other alternative was to fly back to England.