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I've had the same happen, I've not looked into it in much detail but I do the following:
1. Zip up the project folder
2. Delete the project in FlashBuilder (take note of any swcs / src paths etc)
3. Setup new FlashBuilder project of same type
4. Copy everything back into the folder
5. Setup the swcs and src paths
6. Add sdk via windows > propoerties > seach sdk
And when FlashBuider really goes pair shaped (which it often does)
Delete meta, and project settings folders for whole workspace (backup whole dir) and restart FlashBuilder creating new project using same name for each project folder in the workspace.
I'm not really sure if this will will help, because it seems I just can't select any SDK for an Air project. But I will try it.
Allright, so I removed my project from FB4.7 and created a new Flex project.
Had to setup a lot of things again but now its working again !
FlashBuilder (doesn't matter what version) screws this up all the time. There are so many files related to configuration of the workspace, the projects within the workspace and the eclipse environment that it gets messed up all the time.
I never have this problem in other editors Eclipse based editors like InteliJ, Aptana, FDT etc. It's just Adobe growing / extending a tool which has bad programming in it and not bothering to go back and fix the root of the problem before expanding on it. FlashBuilder doesn't get the attention it deserves from Adobe. If they are not careful in the not too distant future when WebGL is supported on all the major web browsers and tools are released to translate WebGL to OpenGL ES iOS and Android applications AIR might see itself becoming a thing of the past. Esepcially when the tools can't even save the state of the projects they themselves created correctly.