If you're calling a .swf from your flash assets folder into your HTML page that is located in root folder, then you need to change your path to the skin, to reflect changing location of your main .swf:
Thanks for the reply, xchanin but how do i change the path to the skin?
It would be where your loader is calling the skin from within the code.
Keep it simple just publish everything to the same folder
then upload the folder to the server then you won't lose your skin.