I've been working with WordPress sites for a while and have never seen anything like this happen...
I just set up a subdomain, did a WordPress install, activated it and then I copied over the plugins and theme that were on the main site to the subdomain. The idea is the sites will look and function the same, but they'll have some different content on them.
So after I did this and activated the theme on the subdomain, I went back to the main site and the theme has disappeared from the admin. The plugins are gone from the admin as well and there are error messages for each one: the plugin does not exist.
And yet, I'm looking at all the files - the plugins and the theme files - in both site folders on my FTP site.