The VMwareVDMDS service is a simple wrapper around an AD LDS install (see https://technet.microsoft.com/en-us/library/cc754361%28v=ws.10%29.aspx). It appears that it is somehow being removed during Windows upgrade, presumably because Microsoft don't support in-place upgrades of that component.
Note that we don't actually support in-place OS upgrades - you should instead install a new 2012 R2 server as a replica, switch everything to point to it, and then retire the original 2008 R2 server.
Mike