I recently solved an odd issue with Skype for Business and an apparent duplicate contact name.
For a single user, when they searched and made a favorite of Employee A, the display name and contact card would appear as Employee B.
At first I thought this was related to Employee A being on temporary layoff and returning, in which time we had assigned that email address to Employee B. However this turned out to be a red herring.
Next I tried to clear the Skype contact cache, based on a Microsoft KB article: https://support.microsoft.com/en-ca/kb/2435699
This didn’t solve the issue either.
I finally solved this by looking within the personal Contacts of this user’s Outlook mailbox. They had a contact for Employee A which contained a bunch of info for Employee B; I presume this was manually created during the layoff period.
Skype for Business was modifying it’s display of the contact based on the personal contact found in the mailbox, rather than strictly what was in the Global Address List.
I deleted that personal contact, restarted Skype, and Employee A once again appeared as himself.