just for the benefit of the forum and other people who might run into this in the future, I'll repeat what I just sent to Ted in an email:
Voxengo (the same guys who make r8brain) makes a great little M/S
plug-in, available for free here:
http://www.voxengo.com/product/msed/it has three modes: decode, encode, and inline. decode is used to
decode a M/S signal to L/R. encode takes a L/R signal and encodes
back to M/S, and inline allows you to adjust the mid-side ratio in a
signal that has already been decoded to L/R (essentially encodes the
L/R signal back to M/S and then re-decodes it to L/R again, but in one
simple easy step).
So, in this case, you want to use the encode function, to encode your
signal back to M/S (which really was L/R that never should have been
decoded in the first place).