The Netapp VSC vCenter plugin was also being used for backups using the plugin through the VIC.
The greenfield installation went without a hitch for vCenter Server 6 environment and hosts were migrated over.
After I upgraded the hosts to ESXi 6.0U2 I had to perform the upgrade of Netapp VSC plugin.
The plugin upgrade process was pretty straight forward with moving the plugin to a new server and pointing to new vCenter server.
Netapp has a pretty good KB out on how to preserve existing repository information on app migration to new server - https://kb.netapp.com/support/index?page=content&id=1011871
After VSC plugin upgrade I ran into a strange issue where ESXi hosts kept randomly disappearing from the vCenter Web client and nothing else getting affected.
Restarted vCenter server and tested with different browsers with no affect.
Disabled the plugin and restarted browser which resolved the issue.
Uninstalled 6.2 and installed 6.1 which seems to have better experience and hosts do no disappear as frequently.
Netapp community has a couple of blog posts related to the issue with no real positive response from Netapp.
Open a case with Netapp and was provide BUG ID 986313 related to issue with no estimate on fix.
The bug can be view on Netapp support -> Tools -> Bug Tools.
Workaround at this time seems to be downgrading or install VSC 6.0 which has the least amount of problems.