All you have to do is create a new Flash builder project and delete your code in the src folder and take it from there.
This is the easiest option and what I will do. These are two different development environments, and you really do not want to import the code from the flashdevelop project folder: instead, duplicate this folder in a new location, and, as I said above, create a new project there.
And, of course, ask yourself if you need to work with two different programs. I have used Flashdevelop for many years, but now I use only Flashbuilder. Go with one and you will find things easier.
Thomas
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