Hi,
If the new URLs are created correctly, you should just delete the old wrong URLs using JoomSEF's URLs Manager and clear Joomla and JoomSEF caches - deleted URLs should be then recreated correctly.
For information on how to delete the URLs, please read the "Working with URLs" section of JoomSEF's documentation:
www.artio.net/joomsef/documentation#d4e928
You can clear JoomSEF's cache by clicking the Clear Cache button in JoomSEF's Control Panel in the Maintenance tab.