When you add or remove collision manually, the NavMesh will not update, even after rebuilding paths. The only way to get the NavMesh to update when collision is changed manually is to restart the editor, and then build paths again.
Found in 4.10 Preview 4, Occurs in 4.9.2 binary and Main CL 2752291.
1. Open the editor
2. Add a NavMeshBoundsVolume to the level
3. Bring in a static mesh (with or without collision)
4. Remove or Add Collision to the mesh (depending on if it had collision to begin with)
5. Build Paths (Notice that the NavMesh isn't updated)
6. Restart the editor
7. Build Paths
Result: NavMesh updates based on manual collision changes only after the editor is restarted.
Expected: NavMesh would update upon building paths when changes to the collision of a mesh are made.
Head over to the existingAnswerHub thread and let us know what's up.