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It is a problem that I have actually resolved for one of my friends. Sometimes due to malicious software, some files become super-hidden. You will not be able to access such files even if you set windows to 'show hidden files'. To view such files you will need to go to 'Folder Options' and uncheck the 'Hide protected operating system files (Recommended)' box.

If you are able to view the files this way, run the following command:
attrib -s -h -r drive:\*.* /s /d (replace 'drive' with the drive letter for the flash drive)

If not, install and run a data recovery software (easily available on the internet)

Run a scan with a reliable anti-malware on both the system and the external drive.

Here’s to Good Karma