Hello Palal and thanks for your reply.

Well I guess I can ask Emirates about this and maybe it's possible to do it that way. Just in case I wanna be prepared to go through passport control/baggage/checkin + baggage/security/immigration.

it seems JAT does not have online check-in. But from what I read below; maybe its possible to check in and go back and get luggage and then submit it up to 30 minutes before the flight...

On JAT's website it states:

How much time before departure should I plan to arrive at the airport?
We advise you to come to the airport on time, so that we can most efficiently take over your baggage, run all the checks and arrange for boarding. You are required to be at the airport 1.5 hours before departure on domestic flights, 2 hours before departure on European international flights and 2.5 hours before for the intercontinental flights.

When is the latest I may hand in my baggage before departure?
The last moment you may hand in your baggage for flight and go through the formalities before boarding the plane is 30 minutes before departure time. After that time the desk closes as well as your flight and it is no longer possible for you to board the plane, for the plane to depart on time.

Can I check my baggage to my final destination?
Yes, you can check your baggage to your final destination, regardless of your changing aircraft and carriers on the route, if it has been agreed between the carriers and if you do not make a stopover longer than 24 hours.