I don't know MediaSurface (and couldn't find much in Google), but the whole point of a CMS is that changes like 'remove one item from the navigation list' are done via a user-friendly tool and saved in a database, not done in code.

If you've already considered this, then you probably need to look at this code:
my $linkslist = str_links($parentlink, '$path,$name,$itemid:', 1, 'order', 'sortnumeric');
where the links are defined. Find the source code for str_links and look at that.

If you're still stuck and aren't prepared to try anything else yourself, get in touch with the people who sold you MediaSurface (they will probably tell you to upgrade). That would be better than continuing to ask questions here without supplying details.