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Where is Linux boot file stored in windows registry?

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And I really wouldn't use a Wubi-install for regular use at all, but YMMV. Create a real dual-boot installation if you are actually going to use this as a server. That is, install Ubuntu or whatever, allowing the install to create its own partitions, without destroying the Windows install.

The new bootloader will either start Ubuntu, or will chainload the Windows MBR, depending on what is selected.

Ubuntu server? I don't know if that has a Wubi package. Check the Ubuntu site.