active theme broken

Please explain me why i am experience difficulties with wordpress lately.
After a failed update to version 4.01 everything went wrong. Layout, widgets messed up, media library gone, visual editor and visual composer gone etc… i could not restore site with the backup plugin i had, so Luckly plugin author restored back to a version so i got the site back again, but still no media library and visual editor?? Everything worked before i tried to update, even the backup was made when everything worked.. So i made a full ftp backup of the site folder, i tried to update my theme with ftp because my auto updater do not work, i got a “active theme brooke”, so i deleted the theme folder and just copied the theme folder backup from my ftp, but still i got theme brooken?? So instead i just renamed site folder to a another backup folder and named the backup as to be the original one, now i got the theme back but all my sidebar widgets gone?? How can this be when i used a completely whole site backup?? How am i suppose to make correct backups so that i will get the exact theme layout back??

How can a attempt to update wordpress version go so terrible wrong??