Try a dynamic EQ or spectral EQ to kill the frequency resonance?

Wah is just extreme EQ resonance swept up and down by the pedal.

Eeeesh that seems like a tall order. I would maybe just look at the signal through a spectrum analyzer in maybe a couple different display modes and look for where the peak frequencies are. or look at a spectrogram and just kind of eyeball a visual average from the heat map. because I'm thinking in order for the sound to still totally fit in it has to either have harmonics and peaks in some sort of tonal way, or oscillate around an average that does.

Are you using a DAW? My first thought was to go by ear with the notes as you hear them, slap tasered duck wah wah on top and then compare the EQ to the guitar stem. If you're hitting the same peaks and troughs you know you can't be too far off target. I realize this sounds simpler than it is.

I fear that this could be an expensive alpha india plugin in the near future.

We’d treat it as a transcription aid rather than trying to reconstruct the original tone. A wah creates a moving resonant peak, so perfect removal is unlikely, but a spectrogram can help track note fundamentals while the passage is slowed without changing pitch. Then compare candidate notes with the surrounding harmony and use narrow, automated reduction only where the sweep masks the attack. Keeping the untouched stem alongside the processed version helps preserve timing and note starts.