You can use the Send To command to copy the documents to the new location and then remove the link to the source file. Once the link is removed, you can delete the document forfrom its original location and have only the one document. Instructions on Office Support: https://support.office.com/en-my/article/Copy-a-file-to-another-library-or-Send-To-location-0bfe3b52-db99-44ed-91c7-140aa9ba3d41