Hello abhishek.kumar@chassisbrakes.com,
From the Reference Manual, I understand that the EXT_SYNC is an input signal. So basically now, you have two inputs connected together, with no signal to trigger them. So the PWM modules would be in sync together but you don't have a signal to sync their reload.

For PWM block, what the toolbox is not doing right now is to initialize the EXT_Sync pin as input for the PWM. So you need to insert some custom code in order to initialize the pin as EXT_SYNC for PWM. I would also try the following approach: Use the reload interrupt from the PWM0, BRD0 to toggle a pin and use it as input on the PWM0, BRD1.

What you could also try is to sync the CTUs from different board since the CTU blocks covers the external in and out pins under the "Pins" tab of the CTU.
Hope this helps,
Marius