Solved! Go to Solution.
I can assure you no "development" is being done using the Flex Application Builder.
You should look into using the Source Code instead of the Application Builder.
I think you can copy your older application into the Application builder's default flexviewers install directory and then it should appear in the list of applications with an "upgrade" label beside it. im not at my work computer to give the exact details but give that a try.
Thats one's got me then. Only thing I can think is maybe that particular application is not a flex app or either the flex version is too old to be directly upgraded by the app builder.