So, just got a 3d printer and it lasted about a week before I ended up getting the MCU Protocol error. Happened to find this post. It was ok, but here is how to do it directly from QUDI ssh connection constantly without the worry of what OS you are running. Only requirement is to ssh into printers os. I use linux so I just created a ssh config for my printer so I do not have to remember its ip. Once in os run the following command:

git config --global http.sslVerify false

All this does is configure git so that it will not be a bother to https the files needed for klipper and moonraker.

then type this:

sudo -i
cd /home/mks
rm -Rf klipper_bck
cp -R klipper klipper_bck
rm -Rf moonraker_bck
cp -R moonraker moonraker_bck
#now remove klipper and moonraker

Verify there is a backup of klipper and moonraker once doe it is now time to remove klipper and moonraker.

rm -Rf klipper
rm -Rf moonraker
# exit out of root mode.
exit

Once this is done it is time to git clone both back into the mks folder

cd ~
git clone https://github.com/QIDITECH/klipper.git
git clone https://github.com/QIDITECH/moonraker.git

This should go get the latest version and download them to the printers os now reboot. I did a full reboot of QIDI via switch at back of unit and waited 30 seconds.

This corrected my MCU protocol error.