Ari

There is a transit are, but I have never seen anyone use it.

Even though security there is not so smooth for those who don't have a Jewish nexus with Israel, I find the staff there can be helpful. If you can grab some airport staff on your way to immigration (before entering the long hallway, but after reaching the rotunda), you might be able to get some help. The staff there is flexible on procedure so long as they are satisfied that you aren't a security risk, and if you don't have to enter Israel, they don't want you entering Israel, so they will likely do everything to get you to use the transit area, even if it isn't open. You might find yourself walked through the airport by security without going through immigration. Or you might miss your flight. The most important thing is to try to check-in online for your LH flight and tell CY at check-in that you are a transit passenger when you check-in. I don't see a way for you not to touch your checked bags (for security reasons) while in transit unless you traveled in on LY.