First, welcome back.
When VeSys Classic performs an analysis it uses all connectivity, even if you are hiding connectivity using AutoCAD layers, therefore you will need to duplicate your drawings (DWG files) and manually de-populate in order to simulate one particular vechicle configuration.
This is unchanged with VeSys 2.0, although the capabilities of performing analysis are greater.
Just to add to Nuri's post above,
Capital Logic, which is a sister product to VeSys 2.0 design, has this capability to filter out parts of the connectivity even from a simulation perspective. This is achieved by using options or configurations to filter out connections and devices on the design dynamically. Background simulation will then use only the 'visible' connectivity for its results.