Yea the gmae Im working on the "independable engine" is Ederon (www.ederon.com). Its a online card game I made years ago but now im working my ass off to get a version that can be uploaded to newgrounds. Right now the swf engine only applies to the game itself. The users not only need to register insite Ederon's website but also work most of their stuff inside the website (like manage their cards, trade, check status, manage their account).
So far while working on it, I managed to create a flash version of the card manager, but Im in deed finding very hard to convert all I've done into one swf. not only that, but in order to load cards information the game need INDEED to be loading constatnly external swf files, since the game has currently about 300 cards right now.
The other stuff I discovered while working on crossdomain files is the ability to come back and foward between swfs, even if, in cases like newgrounds, file gets automatically renamed by a random ID (like 134546.swf) when submited. In this case I made it so when you load the external swf file, it sends the current name (_root._url), then when you head back to the game engine it load the saved name under _level0.
The reason Im doing this is simple: I dont want to "overload" the ram memory with tons of movieclips loaded.
I'll keep this post updated with the progress, and if possible I'll link it here before posting on Newgrounds to make sure its bug free.