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USB storage devices: cleaning up without destroying

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Many, many years ago I had a USB hard drive that I used for moving large files from one PC to another (before Internet/email pipes got wide enough), and one day I wanted to "clean it up", so I . . . . reformatted it within Windows (or maybe it was with Iolo's Drive Scrubber s/w). This didn't just clean it up, it made the device unusable, because, unknown to me, there had been some kind of vital s/w on that hard drive that enabled USB communication, or acted as a file organizer, or whatever.

So, I haven't made that mistake again.

But today I find myself with another USB hard drive and a USB flash memory stick, and when I run anti-virus s/w on them I notice the names of ancient files & folders that I long since deleted and should no longer be there.

Is there a safe way to clean up USB storage devices without destroying them?

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