I am sorry to hear your files are doubled up on your Aurender. The best way to correct is to delete ALL your files from your Aurender and transfer them again. I am not aware of any Aurender tools that allows you to delete duplicates on your Aurender.
I had cover art problems when I transferred my files and had to delete all my files on the Aurender several times. Hopefully, you have your master files stored on a hard drive, NAS, etc. Deleting everything and starting over is the fastest and most accurate method to my knowledge.
You can easily connect your computer to the Aurender file structure using the Finder Go Connect to Server tab (MAC). The iPad settings menus provide the necessary information (IP address, user name & password). This is very easy to do. This is how you delete files on the Aurender and also add or correct the Folder.JPG images files. See:
http://www.aurender.com/page/appguide-transferring#index_macusersThe process is not difficult. Your connect your MAC (or PC) to the Aurender and using Finder on the MAC, for example, locate your files and delete them all. This is the easier and fastest approach to my knowledge. When done, look at the Aurender directory (using Finder) to ensure they have been deleted. DO NOT delete the Aurender file tabs. The next step is to transfer again and double check to ensure they do not get duplicated again. Any questions, please ask.