I had this joined purchase problem the other way around, and I decided to share my story.
1. I had Lion preinstalled, not visible in AppStore purchases
2. Then I purchased Server pack and installed it
Some day I wanted to purchase Lion to bind it to my appstore account (I needed clean install disk for my other Mac since I wanted to switch from 10.5 straight to 10.7).
3. When i clicked - using OPTION key to bypass "INSTALLED" status - on AppStore Lion I was prompted to purchase both Lion and Server. But of course I've already paid for Server on my current machine and was not interested in using it on my secondary machine!
The solution was simple.
4. Close AppStore
5. Run in terminal
"sudo mv /System/Library/CoreServices/ServerVersion.plist /System/Library/CoreServices/ServerVersion.bak"
It causes system version checker to look at pure Lion file "/System/Library/CoreServices/SystemVersion.plist"
6. Launch AppStore and try point 3 again. It allowed me to purchase Lion only and downloaded installer.
7. Run in terminal
"sudo mv /System/Library/CoreServices/ServerVersion.bak /System/Library/CoreServices/ServerVersion.plist"
To restore Server version info.
So it is possible to purchase Lion AFTER Server is purchased without having to request refund for duplicate of Server.
Click "Like" if it helped you