Any way to eliminate a melody instrument in a mono track by deleting its overtones?

I have a track of two melody instruments playing in unison (they're playing virtually the same notes at the same time). Is there a way to eliminate or at least lower the volume of one of those instruments by zeroing in on its overtones/partials/frequencies and deleting them or lowering their amplitude?
I've been attempting this for two days and thought it's high time I ask for help because the process is insanely slow so far. I've tried using filters and EQ but they seem to be too inaccurate. Another problem is that I'm working with Adobe Audition 3.0, so it doesn't have as great of a notch filter as CS6 or whatever the latest is. I've tried going into the spectral waveform view and manually deleting overtones but it's completely time consuming so far. I don't mind spending a couple days doing this to a track, but after two days I've only really gotten rid of the offending instrument on one note. Too slow.
Any advice or thoughts?
Thanks!

You will run into several problems with this, whatever you do. Firstly, unless you are extremely lucky, the instruments will share harmonics, especially if they are playing at the same pitch. Which means that you'll never be sure that you are attenuating the right harmonics anyway. The chances of all harmonics being at the same level for the same note whenever it's being played on an acoustic instrument are about zero - no processing based on that approach is going to work satisfactorily; It's a human performance you are editing, not scientifically determined tone generation, after all.
Having thought about it, there is one other tool that will display the harmonics better (and give you tools for modifying them) is iZotope's RX3. This isn't cheap either, but will give you a clear display of what's actually there if you manupulate its FFT settings. You can also do this up to a point in Audition (although I don't recall how much you can in Audition 3), but I've always found RX's display and tools rather useful for detailed excisions.
Perhaps a little perversely, the tool that's best able to distinguish two different players playing the same tune is the human ear. From what you're saying, I'd be inclined to leave it as an exercise in discrimination for the listener. Not least because in this situation, the nuances of somebody's performing style invariably depend, to a considerable extent, on the way that they've reacted to the other performer. Trying to remove that interplay isn't, IMHO, likely to help at all.
What are the two instruments concerned?

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