I need to convert .swf files to mp4 or other iPad friendly format, while maintaining interactivity, i.e. buttons that can be touched to activate. Can that be done? What's the best way to do so?
Potentially assuming you're not just talking about a "website", you can create an actual "app" of your SWF as well.
Simply start a new mobile project targeting your device (ipad, etc), make sure the stage is the right size for the device and begin importing your other project. Then produce it as an "app" and it will be an installable, interactive mobile application.
For iOS (iPad/iPod/iPhone) you will need an Apple Developer License to produce this however. You will also need to sign up as an Android Developer to access that marketplace as well. You can deliver apps without putting them on the stores if you wish also but that's another process (ad-hoc, enterprise, etc).
As esdebon mentioned, the only other alternative is to see how far Flash Pro CS6 can convert your SWF into HTML5/JS/CSS3 just to get you started but expect to need to know these technologies to really get the job done. There's no truely magical "convert" button.
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