It's been hard to find any info about this but I just had a shiny moltres spawn for the event and decided to wing it for science.
It did not flee when throwing balls at it, I tossed like 4 regular throws and it didnt run and then it broke out at least another 10 times before catching with gold razz + ultra ball. I assume if you are driving the it may flee just like any encounter normally but as long as you are stationary/walking you are good to save your master ball for another day :]
Hope this helps someone out!
by Infel67