At some point there was a bug in Lync 2013 causing records to be duplicated in the contact list. I ended up with hundreds of duplicate records including a few records with more than 100 duplicates each. [more]
Initially Microsoft’s solution was to use Outlook Web Access (OWA), find the Lync contacts folder and delete it. I did this a couple of times, but eventually, access to the Lync contacts folder became protected and could not be deleted.
After a couple of months, when I circled back to the problem, I found a Microsoft knowledge base article KB2916650 which indicated an update would fix the problem, however I was running the updated version. This meant no new duplicates were being created, but the existing duplicate records remained. The only solution aside from the update was to contact Microsoft support.
I contacted Microsoft and they provided a hotfix, the “Lync Contacts Mailbox Cleaner.” There are versions for both 32bit and 64bit systems. The Cleaner needs to be copied to the local system, unzipped and installed. Then launch the Cleaner, choose the email address of the account you want de-duplicated and click the “Cleanup…” bar. You will be able to watch as the duplicates are discovered and deleted.