I have some cx tires that are knobbly (Schwalbe X-one Performance). I want to ride them on mixed surfaces (crushed gravel and paved), I don’t need the aggressive tread, but they’re new and figured I could ride them for a while. I don’t really care if the knobs wear down (a lot). I have new tires waiting for this bike (file tread) and will swap when the knobby tires are spent.

Question - as the knobs wear down, am I increasing risk of flat?

I have routinely ridden tires until I could see a line of bare casing down the center. As they approach that point, flats definitely become more frequent. I think of that as a tire telling me it's time for a replacement. I would assume that your knobbier will do the same but not until they get pretty nearly used up.