OK, I did this a while ago by changing the VID/PID. If I remember correctly I changed the values in boards.txt, connected an ISP programmer to my pro micro, then did a Sketch > Upload Using Programmer. Now it shows up in Device Manager under "Other devices", meaning Windows tried to install it and couldn't find a driver matching the VID/PID. So I don't know if that's exactly the result you're going for.
The reason I wanted to do this is I have a Pro Micro permanently connected to my computer and I was tired of having it clutter up my Tools > Ports menu in the Arduino IDE since I never upload to it. Later I realized you can disable the COM port of the device in Device Manager, which would have been a much easier solution because it was pretty tricky to attach the programmer to the Pro Micro since it was already soldered to a circuit board and doesn't have an ICSP header. Doing that would have allowed me to easily re-enable the port if I ever wanted to update the firmware on the Pro Micro. But it sounds like the solution of disabling the COM port would not be helpful to you.