We can use Fan Fault Mask Registers (12h, 13h) to mask faults on selected fans from asserting the FAN_FAIL output.
Also in PWM mode you can set the target duty cycle of the unused fans as zero to mask the fan-failure detection of that fan.(see PWM Mode Failure Detection section on page 13 of datasheet). In RPM mode, fan failure detection is masked when the TACH Target Count register is set to full scale.