So normally if there's some scripted enemies for a story mission that's placed in the open world they'd simply respawn if you'd kill them before you triggered the mission. However, all the machines (including the Storm bird that initiates a cutscene) can be killed at anytime during your playthrough. I found this out by traveling the map first and then playing the story. The snowy lands with all the stalkers and watchers before hand can be permanently killed too.
This is located below the north most ruins (just above the Vantage). I only found out because once I played the story and ventured there again, Sylens told me there'd be many machines looming around to kill me. But when I arrived there wasn't a single living thing there. Even the Stormbird doesn't show up, as it isn't a Storm birds site.
I found it rather odd that this occured because I almost did this same thing with a side mission however the enemies properly respawned.
I make it sound like a bug, but this was one of the cooler things I found. The Stormbird was so random it felt like a boss encounter in Dark Souls. Just randomly finding a giant beast you know you have to kill but with a small cutscene to ramp up the intensity.
I wish there would be random cutscenes like this more often. For encountering sudden Rockbreakers or even Thunderjaws.