Sitemap and Webmasters Tools – old URLs keep showing up

Hi there. I’m hoping someone can help me here. I’ve got a site that’s over 5 years old and was initially installed in a directory. I moved the installation from the directory to root a couple of years ago, but have realised that the old url’s must still be in the Sitemap for some reason as they keep appearing in Webmasters tools as 404’s.

How do I get rid of these old URLS from my sitemap? I’ve deleted the directory etc from Cpanel, but I’m guessing that there is still reference in the database maybe?

help!