I have managed to choose the wrong duplicates, how do I remove references from the duplicate folder and put them back in my library or does it not matter?
The duplicate records you discarded should be in the Trash bin. Select the Trash bin to view and select the discarded duplicates then drag and drop them into All References (which returns them to your library). (Refer to attached image.) Then you can re-run the Find Duplicates command to search, select, and discard the correct records.
It doesn’t matter if you haven’t deleted them. The group will disappear after you closes it and open Endnote again?