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With DJM-900NXS2, either FX1 or FX2 can be used alternately because NXS2 has Send/Return feature to enable post fader FX, only one FX can be selected.
FX2 is not disabled, but both FX1 and FX2 will be applied to the channel selected by FX1 on the left side of the screen. FX1 -> FX2 is connected in tandem.
The SP1 will continue to function as normal - just use the left side controls and away you go.