If you are using iCloud photos, then yes, all the duplicates are in iCloud - and would be synced back to a new library.
On the other hand if you delete all the photos in your current library by selecting them all (in the all photos view) and then deleting them - they will also be deleted from iCloud.
Then when you re-import the recovered originals they will be re-uploaded to iCloud.
Now I'm going to question what you are doing. How did your freind pull out the originals. If they have been copied from the originals folder inside your library, then I am guessing this will aslo include all the duplicates. Have you checked?
Also you need to be very carful that you do actually have the full size originals, and not (for example) thumbnails or smaller previews.
Before deleteing anything, I'd suggest you make a backup of your library.