Exchange 2013 Upgrade results in Lync 2013 Conversation History no longer updating

I introduced a new Exchange 2013 server into our organization and migrated all of our mailboxes from Exchange 2010 over the weekend.  Mail flow is working fine, Outlook 2007 is connecting, Active Sync on iphones and Outlook Web is all working fine.  However I am having a problem with Lync 2013 IM conversation history posting to Outlook / Exchange after the migration.  I don't have any error messages that I can see in the Lync 2013 desktop client or on either server event log.  I am using a self signed cert for the Lync 2013 product and a GoDaddy cert for the Exchange 2013 product.  I confirmed that my auto discover URL is correct and that all my internal and external virtual directories are configured properly.  Some advice would be kindly appreciated.
CodySystemsAsked:
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CodySystemsAuthor Commented:
Both the Exchange 2013 Server, The Exchange 2010 server and the Lync 2013 server are all hosted internally here on our VMware infrastructure in separate VMs on the same domain and network segment.   The Exchange 2010 server is still online and hasn't been removed from the organization yet, although all email is flowing through our SPAM filter appliance directly to our Exchange 2013 server.
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CodySystemsAuthor Commented:
When I right click on the Lync 2013 icon in my task tray with the Ctrl key held down, I see the following.  The domain and username have been changed:

DG URL Internal;https://lync2013.mydomain.com:443/groupexpansion/service.svc;--;
DG URL External;https://lync2013.mydomain.com:443/groupexpansion/service.svc;--;
Quality Metrics URI;;--;
ABS Server Internal URL;https://lync2013.mydomain.com:443/abs/handler;--;
ABS Server External URL;https://lync2013.mydomain.com:443/abs/handler;--;
Voice mail URI;;--;
Exum URL;;--;
MRAS Server;;;
GAL Status;https://lync2013.mydomain.com:443/abs/handler;--;
Focus Factory;sip:myuser@mydomain.com;gruu;opaque=app:conf:focusfactory;--;
Line;;--;
Location Profile;DefaultProfile;--;
Call Park Server URI;sip:lync2013.mydomain.com@mydomain.com;gruu;opaque=srvr:Microsoft.Rtc.Applications.Cps:nwM2veNjSVSNJTQnnU1XeAAA;--;
Server Address Internal;;--;
Server Address External;;--;
Server SIP URI;myuser@mydomain.com;--;
Exum Enabled;TRUE;--;
Controlled Phones;TRUE;--;
GAL or Server Based Search;GAL search;--;
PC to PC AV Encryption;AV Encryption Enforced;--;
Telephony Mode;Telephony Mode Disabled;--;
Line Configured From;Auto Line Configuration;--;
Configuration Mode;Auto Configuration;--;
EWS Internal URL;;--;
EWS External URL;;--;
SharePoint Search Center URL;;--;
Skill Search URL;;--;
Connected Lync Server;lync2013.mydomain.com;--;
Local Log Folder;C:\Users\myuser\AppData\Local\Microsoft\Office\15.0\Lync\Tracing;--;
Inside User Status;TRUE;--;
Contact List Provider;Lync Server;--;
Pairing State;Lync cannot connect to your desk phone because the USB cable is not plugged in. Make sure that you connect the cable.;Enabled;
UCS Connectivity State;Exchange connection Down;--;
MAPI Information;MAPI Status OK;MAPI Status OK;
EWS Information;;EWS has not fully initialized;
License State;Lync Basic;--;
Hanging Notification Status;;Disconnected;
pChat Room Mgmt Int URL;https://lync2013.mydomain.com:443/PersistentChat/RM;--;
pChat Room Mgmt Ext URL;https://lync2013.mydomain.com:443/PersistentChat/RM;--;
pChat URIs;;--;
pChat Default URI;;--;
pChat Enabled?;FALSE;--;
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CodySystemsAuthor Commented:
I resolved this problem today and it was a pain in the butt. The issue for us was that our SIP domain is user@mydomain.com while our email addresses are user@anotherdomain.com.   The cert on the server was issued to exchangeserver.mydomain.com and as a result, the Lync 2013 client couldn't retrieve the autodiscover data from the new Exchange 2013 server resulting in the Lync client being unable to write the appropriate autodiscovery registry key and the EWS links.

So in Exchange 2013, the autodiscover process is a bit different.  But this only impacts Lync 2013 clients - meaning if you had Lync 2010 clients still around they would connect and the Conversation History would sync fine with no issues after the migration.

The fix was to create a "TrustModelData" registry key with the domain value of our email addresses.  In our case this was "anotherdomain.com" .  I then used a group policy and push it out to all the users.  

After adding the required registry key and restarting the lync 2013 client, it picked up all the correct autodiscovery URLs from our exchange 2013 server and added the needed autodiscovery registry key.  It might take awhile to sync the stale conversation history from your profile - ours processed in batches of 10 at a time.

Here is all the reading required:

http://blog.schertz.name/2012/12/lync-2013-client-autodiscover/

http://uclobby.com/2014/01/03/lync-client-2013-ews-has-not-fully-initialized/

http://lyncuc.blogspot.com/2013/01/lync-and-exchange-web-services-ews-and.html

http://consulting.risualblogs.com/blog/2014/04/15/lync-2013-cannot-verify-that-the-server-is-trusted-for-your-sign-in-address-connect-anyway/
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