Well lets hope you haven't done any irrepairable damage. First off I'll explain what its doing... basically I've got two config files in there.. one for PS3 controller and one for keyboard. It wasn't my brightest idea setting it so confusingly... but it made sense at the time.

Essentially I have rename the keyboard one to something (blight_input.conf becomes blight_input.conf3) and rename the PS3 one to the one that the emulator looks for (blight_input.conf2 to blight_input.conf).

So basically to change it back... do it in the reverse:
mv blight_input.conf blight_input.conf2
mv blight_input.conf3 blight_input.conf

If you've done something entirely wrong and overwritten one of the files.. your best bet is to reinstall as though you are "updating" and download again :P