unset the path for the library used by FullCalendar
When you update a module what ever changes you have done would automatically be over written. if you have just made changes to js then it would be better to add that JS to your theme rather than the module itself. 

You could you the hook_js_alter (On Drupal 7) or jsalter (On Drupal 6) in yout theme to remove the module specific js.