Thank you for your post.
With Instant Web Publishing, you are using a browser, and "Save a Copy" is not available. You need to perform this function from within FileMaker Pro. If the file is being hosted by FileMaker Server, you will need to close the file and then open the file using FileMaker Pro.
How do you open the file if the database is on the server on one computer and filemaker pro is on another computer? How do you get access to the Database if it is normally accessed throught the Filemaker server? Sorry for the dumb question i just don't understand.
You should probably remote to the server box using a VPN, remote desktop, gotomypc, etc etc. Also, if you are on the same network and you have local admin access to that server box, you may be able to "share" your backups folder.
In both cases, you should take a copy from the backups.