I can see only one enable/disable tick box in FS Settings, it's called Enable Joystick. (There's a similar facility in the FS flight window under Options.) In the Assignments and the Sensitivities tabs there is a drop down box in which to select either the yoke or the pedals.
If I tick the Enable Joystick box and then click on Calibrate Joystick, a window Called Game Controllers opens up. There's a Controller column listing two items; the yoke and the pedals, and a Status column with OK for both items. I see no way of enabling or disabling either one separately.
If the Enable Joystick is not ticked, the Calibrate Joystick option is greyed out.
In the Assignments tab I haven't touched anything; both the yoke and pedals work with default settings.
I have FSUIPC3 by the way.
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FSUIPC.ini