I am a little unclear. You say...
mrcjackson wrote
Unfortunately I accidentally deleted the Muse file of a published website and am now rebuilding it.
I take it the "it" refers to the main web site and not your Nabble Forum.
I am trying to copy my Nabble forum onto a new page in my rebuilt site. Using the embedding code it does copy to the web page but it looks like a copy and not as the original.
What the embedding code does is take the current version of your forum and place it in the page where you put the embedding code. It cannot possibly put a "copy" of your forum there. It only knows about the real, current, actual forum.
You probably need to post the URL of your forum here and explain why you think it looks like a copy of your forum and not the real thing.
Also it would not upload to the FTP server.
There is no need to upload a Nabble forum to the host of your web site. Your forum is hosted by Nabble on Nabble's servers. That is why you embed a Nabble forum - so it is fetched from Nabble's servers, and not those of your main site.
Just a Volunteer Nabble Helper - because the nice folk at Nabble have helped me!