I've been looking at how wubildr.mbr works - it finds and uses the first
wubildr by scanning the root of all partitions, in BIOS order. On my
computer the C: drive is the second partition and it never uses
C:\WUBILDR. It always uses the one on my recovery partition /dev/sda1.

So Grub2 is using the existence of /host/wubildr to tell if it's a Wubi
install, but I can delete it and it still boots fine - it's an
'artifact' as cjwatson would say. Therefore it shouldn't harm anything
to have another 'artifact' on the /host partition when Wubi isn't
installed on the Windows partition. If Grub2 considers this a Wubi
indicator, there should either always be a /host/wubildr (or it
shouldn't consider it important at all - i.e. the fact that root is
loopmounted on /host/ubuntu/disks/root.disk should be enough).

Note that when Grub2 does find /host/wubildr - it updates it - to be
compatible with the latest grub changes. The problem is, the one it
updates often isn't the one used to boot. It really should be doing what
WUBILDR.MBR does - check each partition in order and update the first
one it finds (and/or update all it finds). This might also explain the
booting problems we've been seeing lately when Wubi is installed to the
same partition as Windows (bug 682337)

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https://bugs.launchpad.net/bugs/610898

Title:
  grub-pc upgrade renders computer unbootable when Wubi is installed to
  partition other than Windows

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