[Disclaimer, I am relatively new at this so if this is written somewhere else that I have not found please reference me to it]
I was searching ANA for J for my wife in October (TLV-NYC-TLV), I could not find availability for all the segments in J, at least one segment of JFK-ZRH was in Y which would not be great because a. it's an overnight flight and b. it would limit the baggage. So I went about checking everyday only to find more options similar to this one with an SQ segment to FRA in Y but nothing all in J. Then I tried using the multi class/city option and chose TLV-NYC; NYC-TLV manually and lo and behold I was able to find for her return trip OS in J so I booked it and had it ticketed with the outbound flight LO TLV-WAW-JFK in J and the return flight JFK-VIE-TLV in J. In light of my experience I would recommend trying this since for some reason when searching just for a RT flight between TLV-NYC the OS flight did not show up but when searching in the multi city option it apears and I was able to have it ticketed.
I would also be interested to hear if anyone can explain why this is.