Navigation settings out of sync..how to repair

Hello

We have a strange problem where the navigation settings (as of _layouts/AreaNavigationSettings.aspx) are fundamentally different from the real navigation. So the navigation works on the site more or less but the navigation settings controls have just a pair of entries (75% missing). The same problem concerns both global navigation and current navigation settings. 

What is the big problem is that we should change the navigation (hide two entries) but can't do that because te entries aren't there.

Can anyone give any hint:

a)  how to refresh the navigation controls with the "actual" navigation

b) or find out or either hint the reason why the navigation is out of sync.

c) find out any other remedy of the situation not covered by choices a) or b)

With best regards

hank