Using mkvcleaver on the remuxed mkv will also result in a "avi" extraction. Seems it's a one way process - the elementary VC-1 stream is no longer recoverable.
IMO the mkv is not a suitable container for "true" HD stuff. eg. Dolby TrueHD audio does NOT reside in a MKV properly. A Dolby TrueHD track has 2 parts and the AC3 Core part is discarded when muxed in mkv.