What you book in Sabre under one PNR does not necessarily show up in the Airlines Check In System. These systems don't communicate very well. Itineraries need to be amended frequently.
When viewing the VA PNR on virtuallythere.com, it shows the B6 segment. I can't view the B6 PNR on virtuallythere.com, they don't allow it (needless to say the Sabre PNR shows all as well).
Whenever I have made a single reservation on multiple carriers that use different CRSs, the immediate segments preceding and succeeding each airlines segments, also show up in their system (but you can't do anything like selecting seats, ordering special meals etc.) Sometimes, all the segments across all airlines show up on a PNR even though they use different CRSs. Turkish will often show preceding/succeeding flights, but the dep and arr times will show as 00:00, but the flight number and date will be there. At any rate, when this customer checks in with VA, they will likely see that this flight connects on to the B6 flight and may be able to check-in all the way. There's a better chance of them checking through the bags if they see the B6 flight in their system, rather than the pax having to show a separate B6 PNR.