Check-in/out options online are disabled for the time being. Your best option is report at VIE airport as early as possible (even if it is the day before) and explain your situation to the OS ticket desk. Perhaps they would be willing to delete the segment, thus releasing so much needed seat and at the same time letting you fly from FRA. But mind that should you be late with your train connection, it will be your responsibility for the missed FRA-NYC flight.