The comments above include suggestions about chasing notation events differently depending on how they are mapped, adding some sort of reset mapping for some types of triggers, and adding a mapping to change the input note channel based on its notation.
All of these suggestions imply that the mapping should be done at the source, within the MIDI editor, rather than at the destination, at the virtual instrument. That would mean the map file (or whatever UI eventually replaces it) would be loaded from the MIDI editor, rather than from the virtual instrument window.
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