I always face the same problem, hopefuly the FEMAP guys can create a direct method in next release to solve the problem??. The reason why a layer number is not deleted --or reapeared again after doing FILE > REBUILD-- is because some entities still reside in the layer (properties, loads, mesh, etc..).
The layer list tooldoes not tell the user what entities reside on the layer. The method I use to verify what entities reside on a layer is the following:
Create a group with the entities on that layer using command "Group > Operations > Generate Entities on Layer..."
Select the layer in question and generate the new group.
List the group to verify the entities.
Then you know what entities should delete (or move to a new layer), after a layer is empty you can delete it with success. Do a FILE > REBUILD to see that the layer is deleted for sure!!.
Blas Molero Hidalgo, Ingeniero Industrial, Director IBERISA • 48004 BILBAO (SPAIN) WEB: http://www.iberisa.com Blog Femap-NX Nastran: http://iberisa.wordpress.com/