Hello Manish,
I think the API interrupt is not configured correctly, as the BLDC motor project use their own vector table could be kind of tricky add an interrupt.
I did a quick setup with a BLDC projec but I didn´t find any problem.
In this project the API interrupt is toggle the PS5 LED every 11sec.
To enter in stop mode you need to change the flag variable (flag=1) while debugging.
After API interrupt is driven the motor start to spin again.
Please check it and any question just let me know.
Regards,
Alejandro