You should be able to work in the same file and use some functions for opening and saving with Air if you change your Player in the Publish Settings from Flash Player to Adobe Air. To do this you can click on the gray area around the stage or the stage itself then go to the properties of that. From there you click the button labeled "Edit..." under Profile. Then under the "Flash" tab you change "Player" from say Flash Player 10 to be Adobe Air 2.
Now once all that is accomplished your going to want to look into File, URLRequest, URLLoader, and Event.COMPLETE for reading a text file into an array. For saving a file your going to want to look into File, and FileStream for writing a file to disk. If you can't figure it out on your own just let me know and I can provide some more detail on how to work with those.