You shouldn't be doing backups by dealing with the raw MySQL files. It's trivially easy to end up with a corrupted database that way. Consider what happens when you start copying the files to your backup medium - the copy will take a non-zero amount of time, during which the database could potentially write new data in various places, including the parts you've already copied.
Now you're copying a modified file, a mix of old data and new data. This modified copy is almost guaranteed to be corrupted.
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