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The easiest way to accomplish this is to work with a file embedded database: Read the settings from the database when the application loads and save them just before it closes.
With the AIR File API it is very easy to read and write variable length data into and from binary files. The glitch is that you can't add your data in the beginning of the image file where you'd easily find it, but you have to write it at the end of the file instead.
Use the provided bridging interface to expose variables or methods between the sandboxes. For communication between non-application sandboxes use the application sandbox as a proxy between them.