A: thx for all your replies!
Well its a bit of a mess, my program. It has grown/overgrown and was iteratively pre optimized. Not a good plan in hinesight.
What is did was get the atlas and draw it into a newly created texture atlas.
Then I add the atlas to the assetmanager to allow it to loadque.
Then pre store stuff in images and then halfway, after they had been identified, I overwrote the shadows onto the rendertexture.
At the end, I replaced the rendertexture as the texture for the atlas.
I'm guessing that because the pre stored images came from the original atlas loaded in the manager the point to a different texture. So it kept swapping back to the old atlas.
Tried looking into the assetmanager and textureatlas code but decided to stop tinkering.
Doing the overwrite before adding it to the assetmanager works..
The shadowtiles have premultiplies alpha and that gets added tot the atlas in the draw.
Using it would require a complete redesign.
I might give that a try but that would be a standalone project and I don't dare spending the the time required omly to discover that in the end it might all be too slow.
It looks really usefull but I found, a long time ago that writing X*Y 32 pixel quadbatches is far quicker that writing one giant texture. Ill have to experiment with it more I guess.
But also its all in starling v1.8 so a total rewrite might even be better.
For now I'm just trying to finish this beast or i'll get totally demotivated.
But your help helped with that! =)
So now I'm just going to photoshop all the shadows straight into the atlas source pictures. That will take a measurable amount of time and effort but will surely work.