We recently migrated everyone from OCS 2007R2 to Lync 2013. Actually it wasn't as much of a migration as a complete move. I set the servers up separately and did not run the coexistence stuff. I removed all the users in OCS 2007 then added them in Lync. All users are able to sign in however there is a strange issue going on.

When a user attempts to add another user as a contact they search by their name. It shows that users status as unavailable, if you add that user you cannot initiate chat to them. If you search for the user with email address (also their sip login) it shows 2 users, 1 that the status is unavailable and another user that is the actual currently logged in user. Add the user found with email and everything works fine. This is internal users only, one forest-domain that everyone is a member of.

Another thing i did during the migration. Our domain is longdomainname.org and we also have email as shortdomain.com. OCS used long domain and when i setup LYNC i used short domain, i wanted to make things easier in adding users and also with Federation. In Lync topology i have the primary domain as shortdomain.com and alternative as longdomainname.org. 

Any help on "merging" the 2 users when searched would be greatly appreciated. 

I have run update-csuserdatabase and also update-csaddressbook, I see this error in the logs afterwards:

EventID 21054

Users are not indexed in the database that should be.

Expected indexed user count: 0

Actual indexed user count: 593

Cause: User replication issue.

Resolution:

Run Update-CsAddressBook to synchronize all accounts.

I may have it fixed, after writing this post i checked the logs and a whole bunch of events are listed, good events, and everything updated. No errors. Signed out of lync and back in and now if i search by name or email i get only 1 user and its the correct user.

I had added longdomainname.org this morning and ran the update-cs commands and it didn't make a difference, maybe i just didn't wait long enough.

After you change the primary domain and add alternative domain, you also need to add the Simple URL in topology and publish topology. Then run the Install or Update Lync Server System again. You need to add the additional SANs and DNS records for the new SIP domain.

Thank you for the reply, that resolved the issue.