Can't update posts, update settings etc

I have a multisite network enabled network. And i am having a headache from yesterday. When i tried to update my old post, a 404 not found page was shown and even was not able to preview it. Then i searched and got a lots of posts and suggestion which was useless for me. I thought this was due to permalink structure so i changed it to default and instead of solving, it has create more problem as all my pages and posts are indexed in google as mysite.com/my-post and now i can’t revert to custom permalink structure as i am not able to save changes in site settings too from network. So, i have put my site to maintenance mode from yesterday.
I have done almost everything from htaccess edit to disabling plugin but of no avail. I haven’t found a proper solution of this problem, no where in the whole internet.
I need an urgent solution. Geeks please and yes my wordpress version is 3.3.1!!!