What was the folder you ran Decloner on? If you're in the safe mode, the files are moved into the duplicates folder preserving their paths. The first part of the path is volume name. For example, if your main drive is called "Macintosh HD", then when you open the duplicates folder, you will see a folder called "Macintosh HD" there. You can drill down folder levels until you reach the files themselves, and you will then see the folder on your drive they have been removed from, which will allow you to put them back into their original locations. Unfortunately, this is not yet automated, so if there are many such files, you may want to use a Time Machine backup instead.
after running decloner (not realising/considering how important running timemachine first is/was, - i hadnt - & implore you include warnings for users to do so asap), i was in safe mode so its not so bad, however, i preferred "the mess" i had b4... i sorta new where i could find stuff. any suggestion on when automated undo may come about... imo people who run programs like decloner have a very messy life/hd etc & may actually prefer it, to the omg where is that file... feeling you have after running decloner, decloner needs an undo feature imo