I read that the Russians have suspended future Soyuz flights pending an investigation of the Soyuz program, similar to what the United States did following the Challenger explosion. What will happen to the two cosmonauts or astronauts who were scheduled to return to Earth on this Soyuz spacecraft? Will they stay up there for another year or two?
They'll be fine
Russia and US cooperation in the NASA and International Space Station arena is pretty much routine and extra political.
Russian equipment, though extremely durable, is getting to the end of it's efficiency lifespan, and will need upgrades.
I am unsure of the implications of the investigations.
I think the old crew takes the older Soyuz back, just to keep the emergency escape plan "fresh" on the ISS.