Issues recompiling a decompiled Flex project

I decompiled a swf file to edit some ActionScript inside of it but am running into all kinds of issues when I go to recompile it. I'm assuming I have some of the wrong compiler options flagged but after stumbling around through FlashBuilder for a while I just can't find which ones they are. I need to maintain the same file heirarchy as the original file so that the AIR application that utilizes the swf file can read it properly.  Any guidance you all can offer would be greatly appreciated and if there's an easier way to go about doing this I'd love to know about it. I can supply all of the necessary files and go into greater detail if need be.
Original file heirarchy: http://swift.jpe.gs/b0c93f.png
File heirarchy after recompiling: http://swift.jpe.gs/1febf0.png

I doubt FlashBuilder can recompile a decompiled Flex project.  At least not without a lot of work.  Doesn't whatever decompiler you are using also provide a 'recompiler'?

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