If Windows isn't actually using the fakeraid ( and it won't if you don't
have an Intel chipset supporting Intel Matrix Storage ), then it won't
miss the raid signatures.  If it is, then yes, removing them would
render Windows unbootable.

You might have a read of https://wiki.ubuntu.com/FakeRaidHowto.

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https://bugs.launchpad.net/bugs/1175402

Title:
  Failure to find SSD and HDD

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