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If S0 and S1 ports are connected to 3.3V power domain in your design, then only SDHC cards get detected with the default FX3SMassStorage example project, as low voltage operation is enabled by default ( intfParams.lowVoltage = CyTrue)
You need to set intfParams.lowVoltage to CyFalse to disable low voltage operation, so that SDXc cards get detected.