We had a case where, a duplicate prevented call being delivered to Poycom VVX. As you can imagine we spent some time to take logs and understand the issue. but it is simply not visible on that level. When we got traces from the SBA mediation server, it was clear that call is rejected by SFB due to a duplicate.
ms-diagnostics: 4002;reason="Multiple users associated with the source phone number";
Checking in powershell revealed nothing, however in SQL resources table on SBA we discovered records that were deleted, but never left SQL.
Here is how to check this: http://lyncinsider.com/skype-for-business/sql-active-directory-mismatch-prevents-skype4b-user-login/ and http://lynclead.com/?p=324