Here's what we did in a recent upgrade from server 10.6.8 to 10.8 on our Xserves:
Imaged the existing servers, just in case
Backed up all services, archived Open Directory, exported all users & groups
Downloaded & installed 10.8 (it sounds like you have one server, but if you have any replicas, do this on the master first)
Downloaded & installed server.app
Installed all updates
All services appeared to be running with all previous settings intact, but...
We ran into a pretty serious problem with file sharing -- With any luck, you won't need this info, but my notes are below just in case. Hope this is helpful info.
Open directory Master -- All services seem OK.
Open directory Replica:
SMB shares wouldn't mount on either Macs or PCs (authentication errors)
AFP shares initially seemed OK, but we quickly discovered that the service was limited to 10 connections. Users beyond 10 who tried to connect would get an error that the server had reached its max number of connections.
What we tried that didn't work:
Rebooting the server (multiple times) both with the service turned on and off, disabling SMB sharing on all shares and then reenabling it, modifying the maxConnections key in /Library/Preferences/com.apple.AppleFileServer.plist -- it was set to 10, we reset it to 1000 and restarted. This *might* have worked for AFP, but SMB still wasn't working, and we should have had unlimited connections.
Called AppleCare -- the rep advised us to force the server to re-set up the services. To do that...
- Open Server.app, turn off all running services, and quit Server.app.
- Throw Server.app in the trash. Do not empty trash. You'll see a message that Server.app has been moved, or something to that effect.
- Move Server.app back to /Applications
- Open Server.app and it should walk you through the setup as though it was a new server.
- Restart necessary services
This seemed to fix the problem. The AFP plist was completely overwritten -- the new version was binary. All AFP users are now able to connect, and SMB shares are working as well.