Duplicate Cleaner always recommends backing up your files before running any cleanup activity.
As a general rule, you should only delete a file if you know what it is and are sure you don't need it. If you think you might need it, then keep it.
It is always a bad idea to delete files from your Windows and Program Files folders unless you know what you are doing.
The selection assistant can help with selecting files when you have a large list. You can also set input folders as protected to be sure you are removing files from the correct folder or drive.