Hi Chris J
You have to update the Duty cycle too, because it has to be recalculated with every change in the period, so you need something like:
FTM_DRV_UpdatePwmPeriod(INST_FLEXTIMER_PWM1, FTM_PWM_UPDATE_IN_TICKS, new_period, true);
FTM_DRV_UpdatePwmChannel(INST_FLEXTIMER_PWM1, 0U, FTM_PWM_UPDATE_IN_DUTY_CYCLE, 0x4000U, 0U, true);
Hope this helps
Regards