Electronic – Dynamically change PWM frequency with interrupt with STM32

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: one pulse at 745 Hz; one pulse at 1867 Hz; one pulse at 2459 Hz; one pulse at …; one 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 code:

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 train is not perfectly shaped as if the Update Event that update the shadow register happens sporadically. If I'm expecting one pulse with 500 Hz and a second of 700 Hz that doesn't happen. Clearly a constant frequency wave at 500 Hz and 700 Hz is generated correctly. I tried to SET-RESET an output to verify at which point the interrupt is called.

When it fails it seems that an interrupt is called when the PWM is still "high."

Is the PWM the right way to do it or should I use OC or OnePulse mode?