Duplicated modules and drush
Drupal caches the system table with all the module locations, so you'll need to run: 

    drush registry-rebuild


or use the Registry Rebuild module in order to flush that cache after manually updating the module paths in the system table. Alternatively, you could also just manually delete the system list from the cache bootstrap table:

    DELETE FROM cache_bootstrap WHERE cid='system_list';


Sources: 

Overriding and Removing Overridden Modules included in a Distribution - https://drupal.org/node/1974964

Disabling or Enabling modules manually in the database - https://drupal.org/node/157632