I think you can have it as an option whether to use substitutions or an Al Gore Rhythm that will choose the closest available chord if chord is unavailable, then add/mute notes using PRTs. I have done it by adding notes easy enough to play the audio and midi to get the new chord I want but you can't mute a note you don't want, only add, so you would use all midi notes in that case.
If it chooses the closest chord with less notes, then simply duplicates a note or two to get the required chord playing the new midi notes along with the current audio notes, I think that might be the way to go.
I can do this in Reaper by muting notes or duplicating notes.
I don't think it will be that difficult to do, I will think about it some more and maybe post some ideas or if I get a script worked out to do it I'll post some demos.

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