mergeMAXFile will recreate the Layers.
You can also use #mergeDups which will replace existing objects which have the same name.
You can also use #useSceneMtlDups which means the newly merged objects will use existing materials.
example:
mergeMaxFile "c:\\example.max" #mergeDups #useSceneMtlDups quiet:true
--------------------------------------------------------------------------------------
Technical 3D Graphic Artist
Autodesk 3dsMax 2015 - Service Pack 4
--------------------------------------------------------------------------------------