Just go to the boarding gate early when you are in IST, show them your tags, and ask them to check whether your bags have been loaded onto the flight. If you are checked in for the A3 flight then there won't be any issues, at least provided that your bags are transferred properly in Germany. If there is a delay and/or you miss some flights then things will be more difficult.
Entering Turkey to go to the check-in desk will achieve nothing.