Please forgive me, I'm having a hard time understanding the problem.
The TWR program wouldn't have touched your folders.
1st if system restore isn't working, you may have a deeper issue. If it is hanging there for hours, I may very well suspect you have a drive problem.
IF the folder was of installed programs, The programs should still be install and you can find them by clicking the windows icon on the bottom left and then all programs.
I am HOPING your folder on the desktop was a shortcut folder to your work. Storing an actual folder on the desktop is a bad idea as it can be accidentally deleted. I know, I've done it myself. If you did that, the best hope is the folder is in the recycle bin and you can restore it. There should be an icon on your desktop for that.
Otherwise, I am hoping you had a folder shortcut, and you just need to search your drive to where they were store - like my documents or my pictures.