Robin,
Problem resolved.
FTM_DRV_UpdatePwmChannel requires the hardware channel id.
Example:
//FTM_DRV_UpdatePwmChannel(INST_FLEXTIMER_PWM1, 0U, FTM_PWM_UPDATE_IN_DUTY_CYCLE, dutyCycle, 0U, true); /* old code */
hwChanId = flexTimer_pwm1_PwmConfig.pwmIndependentChannelConfig->hwChannelId;
FTM_DRV_UpdatePwmChannel(INST_FLEXTIMER_PWM1, hwChanId, FTM_PWM_UPDATE_IN_DUTY_CYCLE, dutyCycle, 0U, true); /* new code */
Thanks for your help.