I have a Haxe project set up and I have a debug configuration set up to launch the External Swf Viewer.
All of that works great but the debugger doesn't connect back to FDT. I get message in the console every few seconds saying that it's trying to connect.
There is a good chance that you need to add the option to "Add flash debug info" info to the Flash target in the .HXML file. Look at these screenshots: