Cortex-M3 NVIC, When to clear the interrupt flag

After some study, trial and error, I created a simple project for a NXP LPC1768, to test its timer interrupt.
This project contains only startup_LPC17xx.s, system_LPC17xx.c, C-main.c, and timer.c.

C-main.c:

#include "lpc17xx.h"
#include "timer.h"


extern uint32_t SystemFrequency;


int main(void)
{
        SystemInit();

        Timer_Init_n_Enable( LPC_TIM0, (SystemFrequency/8-1) );
        NVIC_EnableIRQ(TIMER0_IRQn);

        /* LED Init */
        LPC_GPIO2->FIODIR |= 0x000000FF;    /* P2.0 to P2.7 LEDs defined as output  */

        while(1);
}

timer.c:

#include "lpc17xx.h"
#include "timer.h"


void TIMER0_IRQHandler(void)
{
        LPC_TIM0->IR = (1u<<0);    // Reset the MR0 Interrupt; Writing a zero has no effect.
        LPC_GPIO2->FIOPIN ^= (1<<7);    // Toggle LED.
}


void Timer_Init_n_Enable( LPC_TIM_TypeDef * TimerX, uint32_t TimerInterval )
{
        TimerX->MR0 = TimerInterval;
        TimerX->MCR |= (1u<<0) | (1u<<1);    // Interrupt and Reset on MR0
        TimerX->TCR |= (1u<<0);    // Enable Timer Counter and Prescale Counter
}

This project seemed to work.

But if I change the timer.c to:

void TIMER0_IRQHandler(void)
{
        LPC_GPIO2->FIOPIN ^= (1<<7);    // Toggle LED.
        LPC_TIM0->IR = (1u<<0);    // Reset the MR0 Interrupt; Writing a zero has no effect.
}

It doesn't work.

If I change the timer.c to:

void TIMER0_IRQHandler(void)
{
        LPC_GPIO2->FIOPIN ^= (1<<7);    // Toggle LED.
        LPC_TIM0->IR = (1u<<0);    // Reset the MR0 Interrupt; Writing a zero has no effect.
        NVIC_ClearPendingIRQ(TIMER0_IRQn);
}

It seemed to works.

I guess that, it doesn't work because I clear the LPC_TIM0->IR interrupt flag too late, so the NVIC generates a pending interrupt for LPC_TIM0->IR.

I don't have a LPC23xx now, so I can't verify my guess.
I guess that, it will still work:

void Timer0Handler(void) __irq
{
        FIO2PIN ^= (1<<7);    // Toggle LED.

        T0IR = 1;                       /* Clear Interrupt Flag */
        VICVectAddr = 0;        /* Acknowledge Interrupt */
}

I think it is usual that, programmer needs to do something to identify which kind of interrupt was triggered, before clear the interrupt flag.

So, if my understanding is correct, how do I know that, I did NOT clear the interrupt flag too late within an ISR?

It is quite frustrated that, I can't even handle a simple timer interrupt properly. Maybe my understanding has never been correct.