Enterprise certificates are lost when Microsoft Lync is started in a RES Workspace Manager managed session. It makes no difference if Microsoft Lync is started managed or unmanaged. The certificates are deleted by Microsoft Lync.
The same issue has also been seen with Microsoft Internet Explorer when browsing to a page that is secured with the enterprise certificates. In this case the certificates are deleted by Microsoft Internet Explorer.
CauseUser Settings for Microsoft Lync or Windows Media Player are configured with the Zero Profile mode "Track any setting changed by application immediately" without any exclusions. As a result, outdated certification information is restored, which influences the validity of the certificates.
Reconfigure the User Settings for Microsoft Lync or Windows Media Player with the Zero Profile mode "Capture targeted items on session end".
An alternative is to create exclusions when the Zero Profile mode "Track any setting changed by application immediately" is used.