It's unfortunate but any registry cleaner can delete things that it shouldn't, according to us the user, because it blindly does what it's set to do. You might want to a) check where you store stuff is not being scanned and b) adjust Quickclean's settings.
Double-click the taskbar icon to open SecurityCenter (or right-click > select)
Click 'PC and Home Network Tools'
Click Settings to expand
Uncheck anything you don't want to be cleaned
Don't forget to click 'Apply'.
Personally I don't recommend using it but that's up to you, it was included in the software by popular demand. Windows has it's own tools for doing most of what Quickclean does.
As Ex_Brit mentioned you have select your QuickClean setting before running it the way he explained.
Also website downloads the web pages/images in cookies and cache location for faster access so if you have accidently selected those locations for cleaning then QuickClean will delete it.
Also some software install/access data from the Temporary folder which if selected for cleaning then it will delete that.
As you can restored the system back so you can check the location of those files and unselect those before running QuickClean.