The moment you disable the sharing, the files will disappear.
Keep in mind, that LinuxMCE provides a pnp server that shares anything it finds. You can rebuild its database in the upnp server screen and your upnp device should see it.
Also keep in mind when sharing files from a upnp device, to have it only share the files in one place, and to turn off any virtualization it is doing, the reason your files are showing up duplicated is because it is sharing those files multiple times at multiple points in a virtual filesystem to make up for the fact that UPNP is a very brain dead protocol in the first place. Making it share the files in one place, eliminates the duplication.