A) Take backup of all the documents that users has uploaded and are in checked out status. B) Delete the documents from the document library. C) Disable the “Require documents to be checked out before they can be edited?” from the versioning page of the documents library. D) Ask the user to upload all the documents again. This time the documents should not be in checked out, due to steps 3 we followed above. E) Once all the documents are uploaded, enable the “Require documents to be checked out before they can be edited?”
Note: If you have any mandatory column to be filled in while uploading the documents the above steps will not work. In this case you will have to make the column field not mandatory and then upload the documents.