I am a Nepali citizen and I have a 2-year Japanese visa, from 2017 to 2019. I want to go to Nepal from Japan with Korean Air, transiting in Korea. Do I need a transit visa?
If you're just transiting – staying airside – you don't need a transit visa to change planes (I suppose in Incheon airport). Korean Air will check your luggage all the way to Nepal (Kathmandu I suppose), and will give you both boarding passes in Narita, and you'll just have to go through airside transit security check.
However, be careful. In Japan, KAL flies out of Narita and Haneda. These flights go to Incheon and Gimpo, respectively. Do not take flights with Haneda⇔Gimpo, as that would require you to enter Korea to go from Gimpo to Incheon, and from Incheon to Gimpo or the way back. KAL should be smart enough not to offer such a combination, but just in case...