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.