Update: There has been no response from SWISS so far. We contacted their SWISS office in Moscow again, but the replies were elusive and indefinite. "It is up to check-in staff to decide".
At around midday I suddenly found out that Aeroflot opened a direct flight from Moscow to Prague tonight. As my relative became extremely nervous with all this uncertain situation with SWISS and I was worried about their health, I decided to book them to this flight instead. My relative is already aboard.
As this technically is no-show, I presume we will have to forfeit the fare and blacklist LH Group.
A relative of mine, a Russian national and resident, was recently issued a D-visa from the Czech Republic. While looking for transportation options for him from Moscow to Prague, we found a flight via Zürich with SWISS.
To ensure that this kind of transit through Switzerland is permitted, we consulted the FAQ page of the Swiss migration office. The English version of the page was somewhat vague as it was not clear if permission of transit pertained to holders of D-visas issued by other Schengen states, so we contacted the Moscow office of SWISS for an interpretation. The staff there renounced any authority on behalf of SWISS in this regard and directed us to the e-mail address of the Visa section of the Swiss Embassy in Moscow.
We complied with the instruction given to us by SWISS and contacted the said Visa section. The reply came promptly and was definitively positive. We were told that the legally-binding French and German versions of the same FAQ page explicitly mentioned D-visas issued by any Schengen state as documents enabling transit. We checked these versions and were satisfied that that was correct.
Thus, we established that this itinerary is permitted, and the ticket was purchased.
Despite all that, one day before departure (yesterday), my relative received an e-mail from SWISS containing the following statement:
Only following nationals are allowed to enter Switzerland, the Schengen area and the European Union from Russia: … Holders of a D-Visa issued only by Switzerland
As shown above, this statement is outright false and directly contradicts the information published on the official Web pages of the Swiss competent authorities. Moreover, as said above, SWISS had already renounced authority in this matter before, and had taken steps to get us informed that this transit is possible and lure us into buying the ticket.
My relative was terribly shocked. I sent a complaint through the SWISS Web site (took unproportionally long time as it takes systematic measures against complaints as it seems), but I am unsure if this will work.
Obviously, this is a clear case for a court, but legal way will take a lot of time, and family matters require my relative to travel as soon as possible. Is there anything else I could undertake to ensure that my relative is aboard tonight?