Recently my site was hacked, malicious theme uploaded and code was totally changed and lost traffic to my blog for almost two weeks. It was easily hacked as my site was on root folder of the hosting space and had a weak admin password. In order to safe guard my blog, moved my site from root folder to specific folder and rebuilt the blog completely new from the scratch. Lucky enough that knownhost hosting company helped in restoring date from the backup database on to new database, but only problem occur was to remap the new URL path, this was able to fix by using the plugin Velvet Blues Update URLs .
My blog site was able to restore or original state. Recommend to read this Moving WordPress site When trying to Create a new post and try to upload the images for the post, the images were upload to root folder of the site but not to new folder.
To fix this issue, is to change default upload folder in WordPress 3.9 .
WordPress 3.9 has a coolest feature to fix this issue without making any changes in WordPress code.All you have to do to change default image upload folder in WordPress 3.9
Go to Dashboard > Settings>Media > change the path of Store uploads in this folder.