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    do {
        if (gpio_num < 32) {
            if (gpio_intr_status & BIT(gpio_num)) { //gpio0-gpio31
                if (gpio_isr_func[gpio_num].fn != NULL) {
                    gpio_isr_func[gpio_num].fn(gpio_isr_func[gpio_num].args);
                }
                GPIO.status_w1tc = BIT(gpio_num);
            }
        } else {
            if (gpio_intr_status_h & BIT(gpio_num - 32)) {
                if (gpio_isr_func[gpio_num].fn != NULL) {
                    gpio_isr_func[gpio_num].fn(gpio_isr_func[gpio_num].args); // my handler is called here
                }
                GPIO.status1_w1tc.intr_st = BIT(gpio_num - 32); // that's the problematic write
            }
        }
    } while (++gpio_num < GPIO_PIN_COUNT);

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gpio_set_direction(GPIO_Pin, GPIO_MODE_INPUT);    
gpio_set_intr_type(GPIO_Pin, GPIO_PIN_INTR_POSEDGE);
gpio_isr_handler_add(GPIO_Pin, my_gpio_isr_handler, (void*) ch);

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static void IRAM_ATTR gpio_intr_service(void* arg)
{

    //read status to get interrupt status for GPIO0-31 - don't have any yet, need to add workarond as below if would have
/*    const uint32_t gpio_intr_status = GPIO.status;
    if (gpio_intr_status) {
        gpio_isr_loop(gpio_intr_status, 0);
        GPIO.status_w1tc = gpio_intr_status;
    }*/

    //read status1 to get interrupt status for GPIO32-39
    uint32_t gpio_intr_status_h = GPIO.status1.intr_st;
    if (gpio_intr_status_h) {
        gpio_isr_loop(gpio_intr_status_h, 32);
        uint32_t gpio_state_before = GPIO.in1.val;
        GPIO.status1_w1tc.intr_st = gpio_intr_status_h; // could case IRQ loss
        uint32_t gpio_state_after = GPIO.in1.val;
        uint32_t gpio_state = (gpio_state_before ^ gpio_state_after) & gpio_state_after; // anything new has arrived?
        gpio_intr_status_h = GPIO.status1.intr_st; //read the new IRQ state
        if(!(gpio_state & gpio_intr_status_h)) // was IRQ lost during status clear?
        {
            gpio_isr_loop(gpio_state, 32); // it's tempting to just set IRQ bit and leave but it could cause exactly the same problem again! so just call the handler function
        }
    }
}

I have to add that it does not actually work exactly as expected as I'm getting these software interrupts (I've also added some debug code to count them) much more often than the issue was happening before fix. Maybe because of the propagation delay in the IRQ pipeline or whatever. Anyway it does the job. I'll probably look deeper into that later.

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const uint64_t INPUT_PIIN_MASK = (1ULL<<GPIO_NUM_34) | (1ULL<<GPIO_NUM_36) | (1ULL<<GPIO_NUM_39);

typedef struct io_isr_param_ {
    uint32_t io_tagle;
    uint32_t io_number;
    uint32_t isr_cnt;
} io_isr_param_t;

uint32_t isr_mode[2] = {GPIO_INTR_HIGH_LEVEL, GPIO_INTR_LOW_LEVEL};

io_isr_param_t io34_param = {
    .io_tagle = 0x1,
    .io_number = 34,
};

io_isr_param_t io36_param = {
    .io_tagle = 0x1,
    .io_number = 36,
};

io_isr_param_t io39_param = {
    .io_tagle = 0x1,
    .io_number = 39,
};

IRAM_ATTR void gpio_isr(void *param)
{
    io_isr_param_t *io_param = (io_isr_param_t *)param;
    if(io_param->io_tagle) {
        //do some thing here;
    }
    gpio_set_intr_type(io_param->io_number, isr_mode[io_param->io_tagle]);
    io_param->io_tagle ^= 0x1;
}

void io_init()
{
    gpio_config_t io_conf = {
        .intr_type = GPIO_PIN_INTR_DISABLE,
        .mode = GPIO_MODE_INPUT,
        .pin_bit_mask = INPUT_PIIN_MASK,
        .pull_down_en = 0,
        .pull_up_en = 1,
    };
    //configure GPIO with the given settings
    gpio_config(&io_conf);
    if(gpio_install_isr_service( 0 ) != ESP_OK) {
        printf("ISR install fail\n");
        return;
    }
    //hook isr handler for specific gpio pin
    gpio_isr_handler_add(GPIO_NUM_34, gpio_isr, (void*) &io34_param);
    gpio_isr_handler_add(GPIO_NUM_36, gpio_isr, (void*) &io36_param);
    gpio_isr_handler_add(GPIO_NUM_39, gpio_isr, (void*) &io39_param);
    gpio_set_intr_type(GPIO_NUM_34, GPIO_INTR_HIGH_LEVEL);
    gpio_intr_enable(GPIO_NUM_34);
    gpio_set_intr_type(GPIO_NUM_36, GPIO_INTR_HIGH_LEVEL);
    gpio_intr_enable(GPIO_NUM_36);
    gpio_set_intr_type(GPIO_NUM_39, GPIO_INTR_HIGH_LEVEL);
    gpio_intr_enable(GPIO_NUM_39);
}