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I remember there was a question like this a few days ago, and I believe it was answer. Look for it, probably it'll help you.
Thanks Michael - I've found this thread about communication between applications: http://forums.adobe.com/thread/429288?tstart=90
I suppose that means its impossible to implement a full drag and drop, although my application would probably be just as good if I implemented a LocalConnection instead. I could get the user to select a node on the tree in the source application, click a button, and have it appear in the destination application, the node could then be dragged within the destination application.
I've also faced with problem of draging between two applications.
It's possible to transmit data between these applications, but it's only a half of the task.
The main problem it to handle mouse release error on second application.
There is no problem to handle that user drag object and move it out of the component - it's ok.
After that we should handle the position of droping this object.
Also it's no problem to handle that mouse is on over component and left button is pushed (at this handle create imitation of starting draging). But it's impossible to handle first mouseUp event. This event don't visible in html (object don't rise mouseUp event) and don't handle in flex. I'm still try to understand the way to get round.
The only way I've founded is to hide flash object on mouseOver event and show an image instead of it until mouseUp event raised. After that show flash and calculate the position of draging. But's if you use tree it's not a good way.