Thanks for your additional info. The problem is that both of this mappings have specific order in the list of all effects so whenever you want to "swap" the MIDI In-Port and Out-Port to select the other mapping you also have to import new FX Settings (by Using bigger Import button twice). This can be solved by correcting the fx order in one mapping to match the second mapping and finally remap all FX Selector commands.
Other tip is, always use Bigger Import button when you are trying to import new mapping which comes with specific FX Settings. Then repeat import process once more to successfully install new fx settings (it's a silly Traktor bug). Finally restart Traktor with your S4 connected and default map for S4 will be added automatically
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