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Is it possible to swap controls during the game by pressing(or holding) a button somehow?
Let's say I have WASD buttons for the Left Stick and a mouse for the Right Stick. Then I press(or hold) a certain button and I have a mouse for the Left Stick and WASD for the Right.
P.S. no autohotkey.

Aside from something like AHK, JoyToKey or Xpadder, no, there isn't a way.

I see. That's unfortunate. I hope that someday LilyPad developer will implement this feature even though only a few games will benefit from having it.