I wrote in an earlier article, Fix for Excessive Duplicate Contacts, that describes how to delete these contacts or folders using OWA or earlier versions of Outlook. This was possible because these older versions did not respect the flag that defines the Lync Contacts folder as a protected folder, like Inbox or Drafts.
You could use MFCMAPI to delete protected folders, as shown below, but this can be cumbersome if you have to do it to many mailboxes -- not to mention the fact that you need to grant yourself full access to the target mailbox(es).
A better solution is to have the end-users do it themselves using OWA in Light mode. OWA Light bypasses the protected folder check and allows end users to delete some or all of the Lync contacts, or the entire Lync Contacts folder itself. The best part is that this works from all versions of OWA, even Office 365!
All you need to do is send a URL to the end-users to login to OWA Light with the steps to delete the folder or contacts:
https://outlook.office365.com/owa/?exsvurl=1&layout=light&wa=wsignin1.0Replace outlook.office365.com with your organization's OWA FQDN, if necessary. By following this specially crafted URL, users can enter OWA Light to clean it up without affecting their current OWA Premium experience.
From OWA Light select the Contacts folder on the left pane. To delete the duplicate Lync Contacts folder click the link for Manage Contacts Folders, then click the Choose folder to delete drop down list and delete the duplicate folder.
If the user wants to delete Lync contacts from an existing folder, select the Lync Contacts folder and use the checkboxes to select them or use the checkbox at the top to select all the contacts displayed. Then click Delete.
Hopefully this will help those of you who were unable to delete these duplicates because you were running a newer version of Outlook 2013 or OWA. Special thanks to Greyson Mitchem for the tip.