What you have to do there, is to speak to both of them, on two sets. And don't you ever get their call signs confused. Coming form the north, Ankara will hand you to Ercan, and you call them AND Nicosia! If Ercan clears you direct somewhere, you talk to Nicosia about it, using the phrase "The other side has cleared me to..., do you approve?" - I've done it a hundred times on my way to Tel Aviv...
It is a sad situation, and it is correct that nother Cyprus is not recognized as a country by anyone, except the turks. But what are you going to do? - Ignore them?
The biggest shame is, that this Island made it into the EU, with a conflict like that boiling there...
Nic