If you log into the downloads section of the corporate pages
https://secure.nai.com/apps/downloads/my_products/login.asp?region=uk&segment=enterprise with your new grant you should see all the software available there (you may also want to setup a user on the corporate support portal so you can obtain patch fixes (as these are often in there rather than the downloads section
http://mysupport.mcafee.com/eservice ) you should get automatic update to latest versions of EPO.
Ideally you want to be running at least 3.6.1 patch 3 (build 3.6.1.231) with the VSE 8.5. (but preferrably epo 4.0 if you feel comfortable with this)
What version of VSE do you actually have installed on the workstations/servers? and how big is your install base?
You may find it easier to just dump the old server and start from scratch then push out a new agaent from a new server, it depends on your setup (and to some degree how easy it is for you to install clients using push or AD or third party tools)