The module functions change the current session only. The new system appearance (modified using ECS) is not saved when the system terminates. So, if anything goes wrong, just reboot to get your original settings back!
If that didn't help (no case known yet, but you never know), simply use the regular "display properties" system dialog to load default windows theme settings and reboot again.
Whenever you use litestep, it is generally recommended to review all RC-files before you recycle into a freshly downloaded, new theme you've never used before. First, check out what it really does!