Seperate the trunk from the leaves as a new object. On the trunk clear Custom Split Normals Data under Mesh/geometry data. Join the meshes.
Custom normals are per-split-vertex normals and not face or vertex normals. Tools that deal with those will not work on per-split-vertex normals. Information about these normals are stored on a seperate data layer that usually doesn't exist on a mesh.
In Maya there is a possibility to "lock" normals. That is not possible to do in blender (yet?) but the current system seems to be solid and predictable in its behaviour.