Visa and dropping the last leg
I have redeemed miles (with a TK partner) to fly JFK-IST-AUH and another ticket to fly DXB-ZRH with EK. The problem is I need a visa to be in AUH and TK does not offer the service, nor does EK, since I will be leaving the country with them. I tried hotels and travel agencies and the price is off the roof. So I was thinking of using JFK-IST, dropping the IST-AUH leg, and buying the IST-TBS myself.
I am afraid the agent might not let me check in since I don't have a visa to my original final destination.
My question is: in JFK can I ask the agent to check me in just on the JFK-IST leg, drop the IST-AUH and then IST-TBS? I will have just a carry on, which make things easier.
Any input is appreciated!