Moving a contrib module from /modules into the sites/all/modules folder
It’s OK (in most cases). Drupal 7 will find new destination of module after registry rebuilding. So, just move folders in proper destination and clear all cache.   

It works for moving modules, but not for disabling and uninstalling. Don't remove module folder before complete uninstalling.

Update: I can move module folder even without disabling that module, because I use Drush for immediate cache clearing. In other situations it will be useful to disable module before moving.