you cannot mix and match files between versions including the web.config file.
If the subdomain is really installed below the main domain root that is not going to work it needs to be a separate root level web site. I know places like godaddy install sub domains below the main site in the file system and they make it seem like a root level site with url masking or url forwarding when it really is in a sub directory but that is not going to work.
A real sub domain like demo.mojoportal.com vs www.mojoportal.com are both root level sites and they are not nested in the file system and that will work because they are completely separate and will not have any conflicts.
But the way some of these hosting companies do it is not like that and it won't work.