In Traktor you can select what mappings relate to what Midi controller hence if you use the Midi Fighter with one other controller or ten other controllers - you won't ever get crossed midi messages ! Yes the ten controllers might over lap in functionality (i.e you could play Deck 1 using any of the controllers) but they won't interfere with each other.
However after re-reading your question - you can't upload the Midi Fighter mapping to the S4 as they will have different midi notes and different functionality.
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