When I changed my settings for the joystick (like you did, left, right, up and down), I couldn't get them back.
How do I reset the controls to get back joystick movement?
You can find the settings here... (C:\Users\[your username]\AppData\Roaming\Godot\app_userdata\Mega Man X Regenesis
Edit the 'inputsettings' json file in Notepad.
The directions will strictly be labeled "down" "left" "right" and "up".
If the joystick doesn't work in-game, you will most likely have lost the "axis" values under those directionals.
Look at the directionals for the menu, ie: "menu_left" etc.
For each menu directional, the "axis" values should still be intact. Copy the axis values into the "specific directional" command values that start and end with "{ }" like in the example in my comment.
After you've copied over the axis values to each directional respectively, save your changes.
Let me know if this helps.