Are you using a splitter to run the StarSense and the WiFi module at once?
From what I understand, if you have everything plugged into the scope at once (StarSense, WiFi, StarSense hand paddle), then connect the bottom of the hand paddle to your computer via USB, then run Celestron CFM, it will see all of the things you have, listed one at a time.
You then basically say "update all" and it will...well, update everything. It's actually pretty slick. It worked perfectly on my setup. I even got an old hand paddle (uses a phone jack instead of the USB port and a true serial port on my old laptop) upgraded. Now, I'm trying to update my late 1990s era CGE mounts, they require a different cable and they run a different program to update them.
I'm glad I kept an old laptop around, now I use it for Megasquirt, to update old telescopes, and to run the SBIG ST-237 CCD camera that I picked up.