Some ideas I've tried -

I've been looking for the specific band I wanted to cut as it changes notes and found a rough estimate of where they hit. Went equidistant from the range of the each frequencies and tried to cut as close as possible to only those frequencies.

Add another Parametric EQ2 w/ small cut on the second note frequency and automate it to turn on/off when those notes are played?

Kinda worked

Like FarleyCZ said keytracking on synth filters can achieve this but if you can't keytrack another cool trick I sometimes do is make like a 4 bar note in the piano roll of the synth I want to use, then do all the EQing I want on it to make that one note sound good and not to resonant on certain bands. Then resample that and put it into a sampler. This way it will key track automatically. The reason the note has to be pretty long is bc higher notes will play the sample faster unless you use warp modes in the sampler in Ableton. But this typically only works well on synths with full sustain and no attack. Of course you can experiment with the ASDR but it will exaggerate certain elements in the sampler depending on the note you select

Hello

A company called SoundRadix makes an EQ that does (I think) what you're describing. It's a pitch tracking EQ that moves with the note/frequency being played. Hope this helps!

http://www.soundradix.com/products/surfer-eq/

At least with Serum it's pretty easy to remove a harmonic as well, using a notch filter, you just have to calibrate the keymapping correctly. Might be useful for removing those major thirds from e.g. FM sounds, which become really dissonant when playing chords. Although at some point you have to ask yourself if you'd be better off with additive synthesis