I use the function CyU3PDeviceGpioOverride.
And i read this:
This is an override mechanism and can be used to enable any IO line as
simple / complex GPIOs. This should be done with caution as a wrong setting
can cause damage to hardware.
If i make a mistake, some PINS on FX3 go to hell or the connected hardware !
It is just talking about mismatch between the hardware design and the function of the pin. Say the GPIO in the board is wired as input and the firmware uses this API and configures it as output. Then this conflict introduces the possibility of the hardware getting damaged (which might get damaged depends on the kind of mismatch).