So, ive been sitting here now for 4 hours and wondering why the heck my application uses wrong methods.
Finally i discovered that the ANE and SWC that are included in my app (under dependencies tab) are not re-loaded.
I mean, ive created new SWC as well new ANE, at least 50 by now, but i still get error in logcat that the method im trying to call is not there.
So as fast test, added Log.d into every method, after every line of code in Java (not a big lib so it was no pain 
) and when rebuilding the AS3 lib
then using my ANEBuilder to compile ANE file, and finally running the application in debug.. i see no log.d's there.
This means, My application project, has cached something. big time and hard!
Now, i've also run both variants under File -> Invalidate cache, but still absolutely no progress, still stuck with a old SWC / ANE
When removing both ANE and SWC from app, intelli complains, (awesome, this must work) and when adding them back under dependencies,
ahh back to square one, same old ANE is compiled into the app.
So, how do i ALWAYS get the latest SWC and ANE into my apps ?
Eclipse and Flash Builder are good at that, just save and everything is done behind the scenes. Also the SWC is updated from eclipse / fb when saving the .as file.
Is there something similar in Intelli ? Like Clean project in Eclipse ?