If you happen to leverage a linked resources directory as your output folder or bin-debug directory for modules and other loaded assets, then you’ll run into problems when trying to export your AIR application for release.
Flash Builder will not recognize linked resource directories in the packaging contents of your AIR application: http://forums.adobe.com/thread/492841
This means modules that you might build to a linked resource directory will not be discovered by AIR when packaging the installer. In order to get around this, you must either use absolute paths (and therefore remove your linked resources) or copy the files to a physical directory in the AIR project’s source path. A simple solution is to create a modules directory in your src/main/resources directory and copy and paste the built modules there.
NOTE: This is just a quick fix and developers should consider using Ant or Maven to do the copying and pasting during the build process.