I managed to do this for MKV files with the help of forum members here, however MKVtoolnix is no go for WMV files.
My Samsung TV and WDTV Live Plus just don't like anything WMA2, so is there anything out there I can use to keep the original video WMV VCI (WVC1), but convert just the audio part WMA2 to mp3/ac3 or whatever other than WMA2?
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It's a couple of steps, but it works...
In the install for Windows Media Encoder comes some utilities, including WM Stream Editor. Use that to demux your WMA2 to it's own WMA file. Then use WM Encoder to re-encode it to a WMA3 file that is more compatible with most devices. Then remux it with the video (in Stream Editor) into a new WMV.