So right now your data is occupying capacity but is not shown when you open the pendrive? You have done pretty good job trying to fix the issue. Have you tried connecting the drive on another PC? Please update your antivirus software and do complete system check. If you the stored data is really important, download a data recovery tool and try to save the data. I leave you a link with some suggestions.
https://ccm.net/download/file-management-53 Once all data is backed up, format the pendrive and try copying files again. If the problem persists, there may be a problem with the device.