[eluser]ray73864[/eluser]
I think i know what went wrong, when i deleted the folders i still had the info in the DB, when i first got it back up and running, i forgot to set the 'index.php' in config.php, so the cache was created without the 'index.php' in the navlinks.
then i went into config.php and put in 'index.php', but by that time the cache had been created, so all that is needed is a way to delete the cache or refresh the navigation cache after altering config.php.
just refreshed the main website now and the navlinks cache has been refreshed, so the links are all working fine now.
