Note that both NOT gate and PWM is not powered in deep sleep mode. As a result the output of these blocks will be '0' in deep sleep. Hence you would see a flicker when you enter deep sleep.
To overcome this, you will need to change the GPIO HSIOM setting to GPIO and set the GPIO output to '1' before entering deep sleep. Another option would be to use the SmartIO block (available on Port 8 and 9 pins) to perform the inversion. SmartIO is powered in deep sleep and hence the inversion will work even in deep sleep.
Let me know if you need further clarification or support in that regard.
Meenakshi Sundaram R