I had a little almost 2 day fun with Flash Builder 4 AIR and the release build.
It turns out that the release build will recompile all added RSL libs removing Robotlegs metadata so the AIR application will not work even if you add the -keep-as3-metadata to the compiler options.

My project looks like:
-Shared libs with robotlegs src code
-Main loader Application using shared libs as RLS
-Module using shared libs as RLS external, building itself to main app bin folder for loading

When debugging or running in the Builder it works just fine when exporting a release build to an AIR package the RSL-s are recompiled by the builder and stripped from the metadata and the Robotlegs app will throw null reference errors.

I've tried different tings to make the code work with RSL-s added -keep-as3-metadata+=... to all projects modified the air-config.xml, flex-config.xml but no luck it seems that there is no way to configure the realase build process.
The only solution is to merge the shared libraries into all projects but that will result to duplicate definitions in the module.

If anyone had a similar problem or has some ideas I'm really interested. The main goal is to create a release version .air file that has a shared RSL with compiled metadata.