Make sure that you go through every group in the console BEFORE you upgrade and remove any assigned packages. There is a bug going from 11.0.6300 to 12x that can remove the AV and NTP component from your clients after you upgrade the server if there is a package assigned with certain settings. The SEP framework will be left in place and you will still see the GUI in the taskbar w/ the green dot but you will not have any protection technologies installed.
We got bit by this and lost AV and NTP coverage on over 2,000 clients before we caught it. Originally tech support assured us it was a "cosmetic" flaw and our machines were protected but after several hours we convinced them otherwise. Finally a tech told us "I have internal documentation on this issue I wish I could share" and he advised is we were basically screwed and had to reinstall all 2,000+ clients.
There used to be a tech doc explaining the issue but I can no longer find it on their website. Good luck, v12 is a mess.