From JPost, 21 Dec 2011, by YAAKOV KATZ:
The [Israel] air force has reestablished a coordination mechanism with Turkey that works to prevent aerial misunderstandings and potential clashes over the Mediterranean Sea.
...Despite the breakdown in diplomatic and military ties, the IAF continued to maintain an open line of communication with the Turkish Air Force to prevent potential misunderstandings when pilots from both countries encounter one another flying over the Mediterranean.
...A senior IAF officer said Wednesday that the coordination mechanism was recently reactivated as part of the countries’ efforts to stabilize and improve ties. Two weeks ago, the Turkish military attache to Israel attended an IAF briefing for foreign military officers at the Uvda Air Force Base on the sidelines of the IAF joint maneuvers with the Italian Air Force.
The officer said that the IAF would also likely invite Turkey to participate in a large-scale international aerial drill that it will be hosting in Israel in 2013. The IAF has significantly increased the number of joint-training drills it holds with foreign countries in recent years.
“There is nothing preventing them from participating,” the officer said.