There is only one VID/PID at one time when running your microcontroller. Which VID/PID your computer sees, depends wether bootloader or sketch is running.
After reset the bootloader is running and is waiting for an upload. During this time your computer sees the VID/PID of the bootloader ( the devicemanager shows the corresponding device e.g. 'Arduino Leonardo Bootloader' )
If it times out ( or after uploading ) your sketch is started. Now your computer sees a different VID/PID and shows another device at a different comport ( e.g. Arduino Leonardo ).
You can still see the bootloader device if you check 'show hidden devices' in device manager.