I just make a copy of my current Flex/AIR combined folder and overlay the new AIR SDK. I never saw a need to keep a clean Flex-only SDK for that and have never run into trouble for the past 4 or 5 SDK updates I've done.
Just be sure to use -rf switches on the cp command (if using Mac bash Terminal) to force the overwrites of existing files of same name and copy recursively the entire directory tree: > cp -rf <newAirSDKFolder>/* <copyOfPreviousFlexAIRSDKFolder> Just don't use Finder to copy the AIR SDK over the Flex/AIR SDK folder. For some reason that causes all kinds of errors that are avoided with the "cp" command. If you don't have a Flex SDK installed already, I suppose you can download it without the installer, though I don't know where you'd find that.
