Hello, if you changed urls on your site, the main issue is not the sitemap.

A sitemap is a mirror of links on your site and its purpouse is reflect exactly all this links that are valid, i mean generate HTTP 200.

If you have an old cached sitemap you can clear the Joomla cache to force a new generation, but the concept of brand new sitemap doesn't exist, because the sitemap is always new being generated in realtime if not cached, or everytime the cache is stale.

if your sitemap doesn't include all 6000 articles, ensure that articles are all published and not expired, and also that in the data source of type 'content' there are no restrictions such as limit to most recent articles.

You don't need to clear sitemap and resubmit in your GWT, the link to sitemap never changes and Google will fetch updated sitemaps every 2/3 days.

To remove old links, ensure that they generate all 404s, in this way Google will remove automatically from the index.

Cheers!

John