The internal flash generally has two parts:
1. User Flash
2. Config Flash
Config flash is not programmable using the mentioned READ/WRITE requests and for changing the configuration mode from UART to I2C, you need to use the USB-Serial Configuration Utility or the command line utility (Refer to CY7C65211 Serial Communication Mode). The mentioned READ/WRITE requests can only be used to write to the user flash area and not the configuration area.
The configuration of SCB0/SCB1 could not be switched dynamically at the run time.
You could configure it with USB-serial configuration utility or command line.
One more thing, you will need to reset the board to let the chip enumerate again to make the new configuration valid.