Hi Nitin,
Sorry for the delay.
Firsty let me clarify my previous answer.
Output of a timer in 16-bit counter mode divides the FlexIO clock by (CMP(15-0) + 1) / 2. Because it toggles the output when it overflows (it is reloaded) and therefore it needs to be reloaded twice in order to complete one output period. But since the second timer in PWM mode decrements on both edges. It can be calculated as if the division factor was (CMP[15-0] + 1).
To your code, I think your calculation is not correct. I don’t see the point of dividing SIRC clock by 64, because 2MHz clock is convenient.
In my opinion, the PWM period should be always the same and only the duty cycle should change.
For instance, period 200 = ((CMP[15-8] + 1) + (CMP[7-0] + 1)).
10%: CMP[15-8] = 179 (0xB3), CMP[7-0] = 19 (0x13)
90%: CMP[15-8] = 19, (0x13) CMP[7-0] = 179 (0xB3)
Then, in order to have clock for 500Hz and 10Hz PWM, only change the value in CMP register of the timer in 16-bit counter mode.
Using 2MHz SIRC clock divided by 1:
2MHz / (CMP[19] + 1) = 100kHz, / 200 (PWM period) = 500Hz
2MHz / (CMP[999] + 1) = 2kHz, / 200 (PWM period) = 10 Hz
The code for 500Hz, 90%:
FLEXIO_Type *base = FLEXIO;
FLEXIO_HAL_SetEnable(base, 0);
FLEXIO_HAL_SetTimerDecrement(base, 1, FLEXIO_TIMER_DECREMENT_CLK_SHIFT_TMR);
FLEXIO_HAL_SetTimerCompare(base, 1, 0x13); // Hex
FLEXIO_HAL_SetTimerPin(base, 1, 0, FLEXIO_PIN_POLARITY_HIGH, FLEXIO_PIN_CONFIG_OUTPUT);
FLEXIO_HAL_SetTimerMode(base, 1, FLEXIO_TIMER_MODE_16BIT);
FLEXIO_HAL_SetTimerDecrement(base, 0, FLEXIO_TIMER_DECREMENT_TRG_SHIFT_TMR);
FLEXIO_HAL_SetTimerCompare(base, 0, 0x000013B3); // Hex
FLEXIO_HAL_SetTimerTrigger(base, 0, 7, FLEXIO_TRIGGER_POLARITY_HIGH, FLEXIO_TRIGGER_SOURCE_INTERNAL);
FLEXIO_HAL_SetTimerPin(base, 0, 1, FLEXIO_PIN_POLARITY_HIGH, FLEXIO_PIN_CONFIG_OUTPUT);
FLEXIO_HAL_SetTimerMode(base, 0, FLEXIO_TIMER_MODE_8BIT_PWM);
FLEXIO_HAL_SetEnable(base, 1);
PWM 500Hz, 90%:

PWM 500Hz, 10%:

PWM 10Hz, 90%:

PWM 10Hz, 10%:

The lower signal is the output of the timer in 16-bit counter mode.
Please try the code.
Regards,
Daniel