Unfortunately there is no way to change the topology on the fly with NI Switch Executive. A better method would be to have two NISE Virtual Devices, one for the 4x32 2 wire configuration, and one for the 8x16 2 wire configuration. You would close out the NISE session from VirtualDevice1, and open a session to VirtualDevice2 that references the same hardware. Of course, you would need to make sure that the external connections are connected properly, but this should change the topology for you.
Note: Closing the NISE session for VirtualDevice1 and Opening the NISE session for VirtualDevice2 will reset the switch module and cause all previous connections to open.
Hope that this helps!
Frank, National Instruments Switch Product Support Engineer