I do not know if it is related to 2018.3 but I have NDK 16 set up in 2018.3 and no NDK defined in 2018.2. And 2018.2 complains about wrong NDK version everytime it recompiles. In addition to no having NDK path defined in 2018.2 my project is not an android project.
Could you share the editor log from 18.2 with the NDK error when you are not building for android?