Clone Disk missing folders

I have Acronis True Image 2013 Build 6514, I Clone my primary hard disk a few days ago and keep it as a backup and I needed to fix my outlook calendar and the folders are missing on my clone hard disk. I just wanted to copy the folders back to my primary hard disk and presto, it should fix the problem. But I just notice I am missing two folders on the hard disk and one of them is my outlook folder containing my outlook folder.
I have been using this software with no problems and I am not getting any errors.

Is this software not catching hidden files. (AppData\local) and (AppData\Roaming).

Please advise...