That's an interesting article. Whenever I read something about the Fermi Paradox, I always have the same thought. I imagine walking through a park and taking a few turns off the beaten path. I reach an area that seems pristine, watch the may flys buzz in the sun light, then go home at dusk. 3 years later, thinking fondly of my secret area of solitude, I return to find it is untouched, may flys still buzzing in the sun light. From the perspective of the may flys, who only live for a day, it's been over 1000 generations since the lumbering giant gazed upon them, leaving the gift of the apple core which generations feasted and grew fat on. Or they didn't notice me at all, walking past they mistook me for an odd tree and made no note of me in their history. Fermi assumes too much, that aliens exist on our time scale, that we would recognize them when we see them, that they haven't been to earth but obscured in ancient stories. It bothers me as a lack of imagination.
Your story is appealing, and this subject is so friendly to speculation it's possible to turn it around. Since you are aware of the flies, and they are not aware of you, I understand that the flies represent humans, ignorant of forms of life very different from their own. But there is no Flymi Paradox. Fermi does not ask why we can't see every form of life that exists. He asks why we do not see any form of life outside our local area. Our local area is teeming with diverse forms of life, from microscopic to visible from space, with lifespans measured in hours, years, and centuries. The flies are surely aware of the swallows that prey on them, the raccoons and squirrels that leave tasty morsels behind for them, the grass and shrubs and trees that surround them. In every direction, at all times, as far as they can perceive, they are surrounded by life, even though their oral history may not preserve memory of the occasional warm-blooded biped passing through (just as humans are ignorant of species that are too small to see, or live too far in the past, or in habitats too inconvenient to observe). The Flymi Paradox would present itself if the flies detected vast areas apparently similar to their home territory and capable of supporting life, yet inexplicably barren.