PWM with different frequency

Hello,
i'm using an stm32f4 to control a stepper motor.

I'm not sure if i need PWM mode or OC Mode or OnePulse Mode.
I can generate a fixed frequency PWM wave but since i need a particular acceleration/deceleration i need to vary the frequency of the wave with a ramp.

Something like: - 1 pulse at 745hz - 1 pulse at 1867hz - 1 pulse at 2459hz - 1 pulse at ... - 1 pulse at ... - N pulses at ... (constant speed)

Right now in the callback HAL_TIM_PWM_PulseFinishedCallback i'm issuing new TIMx->ARR and TIMx->CCR1 values based on a given logic.

Here is my init

void MX_TIM9_Init(void)
{
    TIM_OC_InitTypeDef sConfigOC;

    htim9.Instance = TIM9;
    htim9.Init.Prescaler = PSC; // Get clock to <freq> Hz
    htim9.Init.CounterMode = TIM_COUNTERMODE_UP;
    htim9.Init.Period = 1582; // useless since it is varying
    htim9.Init.ClockDivision = TIM_CLOCKDIVISION_DIV1;
    HAL_TIM_Base_Init(&htim9);
    HAL_TIM_PWM_Init(&htim9);

    sConfigOC.OCMode = TIM_OCMODE_PWM2;
    sConfigOC.Pulse = htim9.Init.Period / 2; //useless but always 50% of CCR1
    sConfigOC.OCPolarity = TIM_OCPOLARITY_HIGH;
    sConfigOC.OCFastMode = TIM_OCFAST_ENABLE;
    HAL_TIM_PWM_ConfigChannel(&htim9, &sConfigOC, TIM_CHANNEL_1);

}

void HAL_TIM_PWM_PulseFinishedCallback(TIM_HandleTypeDef* htim){
    if (htim->Instance == TIM9){
        // logic
        TIM9->ARR = v;
        TIM9->CCR1 = v/2;
    }
}

int main(void) {
    //other
    MX_TIM9_Init();

    //logic and if needed
    HAL_TIM_PWM_Start_IT(&m->htim, TIM_CHANNEL_1);
}

What i'm noticing is that the wave is not perfectly shaped as if the Update Event that update the shadow register happens sporadicly.
Is the PWM the right way to do it or should i use OC or OnePulse mode?

Regards,