Downloaded Xcode 3.2.5 and iOS SDK 4.2, installed and opened an old project. Got error note Base SDK Missing, as expected. Nothing to worry about!
Select project, press Command-i to view project info, find Build - Architectures - Base SDK and select the new "Latest iOS (currently set to iOS 4.2)". Close info - and nothing happens!
Select Targets and your application, press Command-i to view target info. You might have overwritten default project settings by mistake earlier. Check what is Build - Architectures - Base SDK. Should be same as you just defined for project. Close info - and nothing happens!
Close Xcode, reopen your project - and Base SDK is set! Didn't really expect this kind of new features with the update...
Update: No need to close Xcode, just toggle some settings via "Overview" popup at top left corner. For example change "Active Configuration" to Release and back to Debug. Usually that's enough, though sometimes target device has changed, too. Verify all "Overview" selections after you've done this.