A legacy issue with MESH is that the impervious class used to be handled differently. Here's an explanation of how to create your files regardless of whether-or-not you have an impervious class.
1. Use Kenue to turn your DEM and geotiff files into a map file (make sure the last GRU is the impervious/urban class if you want your new_shd.r2c file to be compatible with WATFLOOD). Edit the .map file to include an additional "empty" landclass as the final landclass.
2. Run the bsn.exe program to create the new_shd.r2c file (make sure you answer "y" to the question about whether or not it is correct that the number of classes now includes the impervious class)
3. Create the MESH_parameters_class.ini file with the number of landclasses you need. (i.e. one landclass less than what is in the .map file). The MESH_parameters_class.ini file and the new_shd.r2c file should NOT have the same number of classes
4. If you already have a MESH_drainage_database.r2c file, manually edit (with notepad++ for example) the :ClassCount to be one greater than it already is, and add a new :AttributeName as well as an extra block of zeros at the end of the file.
5. Gently remind the standalone MESH development team that they need to fix the code and documentation.