Actually, the same problem persists in v2.5 also.
I have done custom navigation mesh class (from RecastNavMesh) and made it blueprintable. Everything works as expected, except, every time I open my project, Nav Data Class and Preferred Nav Data properties (in supported agents) are showing “None”. The fun thing is that the DefaultEngine.ini file has these setting correct.
It’s very annoying and time consuming to set these setting over and over again, each time i’m opening my project. As the generated nav mesh is also deleted, i mush open ALL my levels and trigger the navmesh generation.