Can't importing a Flex project within a Java project

Hello,
I am taking over an existing project from a vendor that is no longer involved that has a two Flex projects inside of the Java project. I am using the Flash Builder plugin inside Eclipse. I have checked out the Java project locally and brought it into Eclipse and it builds perfectly. My issue is in getting Flash Builder to recognize or import the two Flex projects within. I have tried various methods of adding or importing the Flex project into my workspace but they all break the file structure in one way or another and thus make it impossible to compile in the structure that was set up. It looks like Flex was set up to build into the webapp/flash/projectname/build folder. No matter what I do Flash Builder creates other output folders or project folders. I have tried add project type, import and new. The original .project and .actionScriptProperties files are there but Flash builder seems to ignore them and create new ones elsewhere.
The file structure looks like this:
javaproject
     src
          main
               Flex
                    flexprojectone
                    flexprojecttwo
               java
               resources
               webapp
                    flash
                         flexprojectone
                              build
                         flexprojecttwo
                              build
                    internal
                    lib
                    themes
                    WEB-INF
Thank you
Greg

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