The Mid/Side decoder in the recorder can be employed either at the input stage (in which case you are recording Left/Right signals instead of Mid/Side), or the monitor matrix (record as M/S, yet provide L/R out to headphones) and/or main and sub out matrixes (record as M/S, yet provide L/R out to main and/or sub outs).
If you've already recorded the matrixed Left/Right, you can convert it back to Mid/Side again. You can do so either via direct playback from the machine using the Mid/Side decoder in the machine on the playback side (M/S > M/S decoder > L/R) [edit- that does not work], or in your DAW (sum L+ R to create Mid; sum L - R, inverting polarity of R to create Side. Sum/Difference = Mid/Side).
That way you can "re-tweak" the Mid/Side ratio slightly if necessary when converting back to L/R again via another pass through a M/S decoder.