Hello, I am trying to use the Thrustmaster T.Flight Hotas 4 for Microsoft Flight Simulator and while it works fine for the most part. MFS is not detecting the throttle nor is it detecting rudder movements. Any idea what it could be?

Do the throttle and rudder show up in the options/controllers window (you should see the bar move).

If it moves there but is not in there when you fly, then it has nothing to do with your controller but is just a MS2020 fault that comes and goes. The first thing to try is to move it to a new USB port. If that works, try moving it back to the port where you wanted it. Next thing is just reboot Windows. Although sometimes just rebooting the sim itself will work (FS 2020).

I think it is a USB thing , Windows is turning off a USB port. I think your throttle and and the metal ears rudder on the throttle are a separate USB than the stick twist rudder and elev/aileron, even if both controller of the HOTAS plug into the same port on the computer.

Control Panel Device manager you can uncheck 'allow Windows to disable USB ports' in properties/power management. There are lots of these in device manager. Uncheck them all: 'Human Interface Devices' and 'USB Controllers'

I have the exact same hotas 4 and it works fine. Only thing I did extra was to set it to 7\8 axis in the Thrustmaster app rather than 5\6 as this then split the rudder from the trim controls. But that would not effect your lack of throttle control. 

Option to consider - use FSUIPC to assign your controls, instead of directly in the sim. FSUIPC provides better calibration options and access to functions not assignable directly in the sim via so called "offsets".