that poses a problem in modules that are in development.
if the Devs change the original input.lua and you copy an old version with your mods back, you might miss out on updates (happend in the harrier and the TDC-axis slew).
the "trick" that worked for me is , after an update, imidiatly(!) exit the game and copy my modified lines back into the default.lua.
never had to redo any keybinds
this post was made without coffee