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Last year I flew from Birmingham International (UK) to Istanbul AtatΓΌrk Airport (TK) for my final destination, which was Suvarnabhumi Airport (TH). When checking in in the UK, I was given a boarding pass for my flight from Birmingham to Turkey. Once I arrived in Turkey I went through the transfer funnel, through security (I think immigration I cannot really remember) then into the transit terminal.
Once there, I went straight over to the Turkish Airlines desk, handed them my passport and they printed a boarding pass right there for me. This sounds relevant in your case, don't worry after all you are in Turkey. They can and will be able to issue you a boarding pass in the transit lounge (after security).