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My best guess (and I'm still not sure but taking an educated guess) at what happened is, while I was deleting, I accidentally selected *both* the left and right sides, instead of just the.
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It costs money but it's worth it - both Windows AND Linux versions. However a nice GUI program: Beyond Compare from Scooter Software is a native Windows app that will compare entire subdirectories or even entire disks and will show a GUI of changes / mods / missing / extra files. How to verify that the files are copied without problems? Checksums are better long term.
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