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When an element is nillable and has a type that is or is derived from ID, IDREF or IDREFS, section 3.15.5 of the spec is not clear about what happens to the ID/IDREF Table: whether such element is ignored, or its actual value should be take into account (which doesn't seem to be possible).
Note, the corresponding bug for XSD 1.1 is bug #2040; bug #9923 is also relevant.