As far as I experienced, if the Muse Sites are in a different place than they were originally, Muse asks you wether you want to drop them out of the list or not as soon as you start Muse.
That should help
Not quite clear, what you want.
And? What means „several sites on my Muse index page"? Links? Or what?
But we will never find out, if MCLSmith doesn`t respond anymore.
If you want to clear the welcome screen:
Click [File] > [Open Recent] > [Clear Recent]
That will clean your welcome screen.