Hi Kevin,
So this is not officially supported with 4.6, nor is it for 4.7, so do so at your own risk. But you can actually setup the Installer package to do a couple things to bypass that error in Server 2012 and 2012 R2.
1. Right click on the setup.exe file, and select "Properties"
2. Click the "Unblock" button on the bottom right if it exists.
3. Go to the "Compatibility" tab. Select the checkbox that says "Compatibility Mode" and then tell it to run in Windows 7 mode.
4. Lastly, select the checkbox in that same "Compatibility" tab that says "Run this program as an Administrator".
I personally tested this with CSM 4.7 in Server 2012 R2 and got it all installed and it worked flawlessly.
As for your issue with restores, while I can't speak to whether it's supported, I can tell you that thus far, I've not been super successful with trying to upgrade CSM from a different server, to a new one without doing a clean install, and then rebuilding my policies. I typically will just import my largest firewall in terms of config so it sucks in most of the objects/ACLs etc.., then build global policies and configs from there, and import 1 at a time to do the cleanup. It's painful, but it at least makes me feel like it's 100% clean.
Let us know your results on the above!
