It only will, if you have dublicates physically on your Hardisk you removed from MCs library previously. There was a bug longer time ago in MC12 which causes dublicates in library with the setting I recommended, but this should have been fixed in the past...
To be absolutly sure you should do a Backup using File -> Library -> Back Up Library... If ANYTHING is wrong after doing an import you can easy go back to the old state using File -> Library -> Restore Library....