Ok so you just did the wordpress update and now you are getting 404 pages,
well there are bunch of things you can do,

1. go to Admin -> Settings -> permalinks – The permalinks page fires $wp_rewrite->flush_rules(); each time the page is visited, so it’s not even necessary to save.
2. save than delete your .htaccess file

i bet you have done all of this already,
well i have found a fucked up problem which i did not think of, one of my projects uses many custom post types,
if your custom post type initilization name containes capital letters this update will lend you on 404 pages
does not matter how many times you rewrite your permalinks

this is what i did

i backed up my database, opened it in a text editor, than just did find replace on all the instances of the capitalized custom post names,
than i did a find and replace on my functions.php file,
than i replaced my databse with the fixed one and replaced my functions.php file,

all works now,

also make sure you have ’rewrite’ => array( ‘slug’ => ‘yourcustompostname,’with_front’ => FALSE),

in your args array for the register_post_type(‘yourcustompostname’,$args);

hope this helps