Because it's MIDI, in editable notation mode you could right-click on the unwanted F# and delete the notes, then freeze the track to stop the notes being regenerated.
You can also change the pitch of the note instead if you wish.

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You can do something similar for RealTracks using Playable RealTracks (replacing some of the RealTracks with MIDI).

Also, check your setting for Option > Preferences > Arrangement to see if changing the setting of Natural Arrangements makes a difference.


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