If you open a model created in the 3.5a version of COMSOL Multiphysics, a Mesh Object node representing the mesh appears in the meshing sequence to handle backward compatibility.
The Settings window for the
Mesh Object node (

) contains the follow section:
If you save the model as a .java file, COMSOL Multiphysics
uses the filename specified in the
Filename field to determine the path to a mesh file, containing the mesh, that appears together with the
.java file. The software uses this mesh file when you run the resulting
.java file. By default, the filename has the prefix $FILENAME$. If the filename starts with this prefix, COMSOL Multiphysics puts the mesh file in the same directory as the
.java file. It is also possible to remove this prefix and specify the full path to the mesh file.
To create a new mesh for a geometry with a Mesh Object node in its meshing sequence you first need to delete the
Mesh Object node.