For example, assuming a 5.1+downmix input MOV file,

ffmpeg -i in.mov -filter 'channelmap=map=DL-FL|DR-FR' out.wav

will create an output WAV file tagged as stereo from the downmix channels of the input.

To fix a 5.1 WAV improperly encoded in AAC's native channel order

ffmpeg -i in.wav -filter 'channelmap=1|2|0|5|3|4:5.1' out.wav