Richard,
You may take a look at some advanced eq plugins targeted at mastering. The
Voxengo Curve EQ may be able to do something like you mention. It is a linear phase eq that displays both the input and output FFT spectrum. I believe it has an invert eq curve function, though it's been awhile since I played with the demo (which seemed nicely transparent and worked very well for my recordings BTW, I'll probably purchase a copy). It has a couple additional features that may apply to what you are trying to achieve which I did not experiment with but sounded interesting. I just copied the blurb below from the site linked above:
Besides the aforementioned features, Voxengo CurveEQ implements SpectruMatch spectrum matching technology that allows you to perfectly transfer a spectrum's slope from one recording to another. This allows you to `copy' a frequency balance of existing mixes so that other mixes that are still in the works will sound better. This technology also greatly helps in music disc mastering, since using it allows you to easily lessen any dramatic differences in the area of frequency balance between various tracks.
GearMatch technology allows you to transfer impulse responses of high-end analog audio gear to your digital audio, while allowing you to adjust frequency response freely.Sounds similar. Not sure if it allows for capturing and applying the
inverse of the response. In any case, the developer is quite responsive to questions posed on his message board and was quite helpful when I was looking for a tool to make a constant phase shift across all frequencies. Worth a look. If something like that doesn't work you may need to venture into the more arcane world of impulse response capture and manipulation or more involved professional tools like the analysis stuff Chris mentions or dedicated FOH balancing EQ tools with measurement capabilities, all of which are out of my league.
Though I have no direct experience with this, I'd also stress Chris's points about an strong requirement to use the same mics, absolute mic position and house eq settings to get anything like decent results with this type of manipulation.