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Now I have a wubi partition on my HDD that I can't remove via add/remove programs. Would simply running the latest wubi install remove my existing wubi partition?

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I have a feeling that by "I have a wubi partition" the author means "I have an Ubuntu menu entry in GRUB boot menu which I can not remove since I re-formatted the Windows partition which used to host the Wubi install". –  Sergey Apr 30 '12 at 2:28

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If you have done installation using wubi, it should have some files on the hard disk and visible in windows. You can just delete those files.

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