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In that case all that is left is to uninstall, clean and reinstall your CE version... That is the only way to guarantee your tree is working properly. Building a kernel might still work, but you just never know what binaries are linked now as some will have been built from different source than what was shipped by MS (on either the official DVDs or in update packages later installed). Reinstall if you want to build qualified, known-to-be-good kernels.