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Would like to defrag Vista seperately,understanding that Ubuntu does not need it. While Ubuntu files are included on the c drive will it cause problems?

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Wubi creates a virtual disk (the same as any VM, like VirtualBox or VMWare) which can be defragmented within Windows just like any other file. Feel free to defragment in Vista - it won't affect wubi.

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    You may even get better Wubi performance... (you certainly won't experience problems) – 8128 Oct 25 '10 at 7:50

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