Finally, after some experiments I found what was going wrong, The problem wasn't really with the code, as I configured the PWM mode as Mode 2 the pulse is negative instead of Positive with PWM 1. So The signal is actually inverted. At duty cycle set to '0', the pulse will be at peak amplitude and LED will glow ( with active high configuration), also because of the fast blinking the decrease in the intensity is not clearly visible even at 50% duty cycle. I changed the duty cycle to about 80%-90% and I got the LED getting less illuminated.

From the user manual of the board : https://www.st.com/resource/en/user_manual/dm00231744-stm32-nucleo-32-boards-mb1180-stmicroelectronics.pdf

PA6 is connected to PB6 through the jumper SB16 (which is its default state):

*Arduino pin A5 being Stm32 pin PA5

Maybe you have PB6 high, pulled up or in Hi-Z state and that's causing the signal to float @ 2.4V.

If that's the case, you need to remove the 0R resistor on the board :

I have run into a similar issue very recently, with an H7, but ST likes to reuse their peripherals.

Advanced timers (TIM1 and TIM8) have a built-in break option, for cases where you'd want an external input to be able to step the PWM output without interacting with the firmware. You must disable that break for TIM1 to output anything.

In general, if all you need is a basic PWM, I advise against using TIM1 or TIM8, they are quite complicated for timers and will bring you only pain. Use TIM2 through TIM7, or anything above TIM9, assuming they have PWM outputs.

You don't need the complexity of chained timers to achieve this on STM32. You can either use TIM_RCR for certain timers to have a Nth UEV interrupt change polarity, or you can simply implement a software counter in an UEV interrupt handler to emulate RCR.

But the most important thing is to use preloaded OC register control for correct glitch-free operation. There are two modes of preloaded control that you can use (TIM1 as an example):

1. Output in PWM mode with preloaded OC control:

TIM1_CCMR1 = TIM_CCMR1_OC1PE | TIM_CCMR1_OC1M_PWM1;

In this mode, TIM_CCR1 is preloaded, i.e. any changes to it will be applied after UEV (update event). In other words, every write operation changes the next duty cycle, not the current.

This mode is mandatory for glitch-free PWM mode operation.

2. Preloaded commutation control:

TIM1_CR2 = TIM_CR2_CCPC;

In this mode, changes to certain bits in the TIM1_CCMRx and TIM1_CCER registers are preloaded. The values programmed are applied upon COM (commutation event) which can arrive either as a trigger or via TIM1_EGR = TIM1_EGR_COMG.

This mode is required for glitch-free commutation control.

In your code, you change polarity via TIM2_CCER without any preloaded control enabled, hence glitches are unavoidable. It's also worth noting that your code has excessive latency due to weird statements like while(TIM2->CNT);. In correctly written code, changing polarity even without preloaded control will still give good results albeit not ideal.

The initial requirement is: The original firmware generates PWM (duty cycle 50%) and every 8 cycles inverts the signal

It's hard to come with a good solution without further details. It's unknown, for example, whether duty cycle is always fixed at 50% or should change. If it's fixed, we can come up for instance with another approach - use timer PWM mode with preloaded OC control at twice the frequency and have duty cycle alternate between 0% and 100% in a preloaded fashion. At the 8th iteration, alternation changes.

A very simplified interrupt-based example:

void tim1_up_isr(void) {
    static int n;
    if (!(++n & 7)) return; // Change polarity every 8th iteration, i.e. do not alternate
    TIM1_CCR1 ~= TIM1_CCR1; // Alternate duty cycle between 0% and 100%
}

...
TIM1_BDTR = TIM_BDTR_MOE; // Enable main output
TIM1_CCMR1 = TIM_CCMR1_OC1PE | TIM_CCMR1_OC1M_PWM1; // PWM1 mode, buffered CCR1
TIM1_CCER = TIM_CCER_CC1E; // Enable output
TIM1_DIER = TIM_DIER_UIE; // Enable UEV interrupt

The above is just an example of the preloaded PWM control concept and in no way is the most efficient code.

In the ultimate case, when duty cycle can change and on-the-fly polarity/mode change is required, the only correct way is to use both preloaded commutation control and PWM mode with preloaded OC control.