I've created the outline to a story involving human beings colonizing Venus, or rather the atmosphere at an altitude of approximately 51 km. Through advanced medical techniques, the first colonists have been totally and permanently altered to thrive at that altitude and even to build floating structures. They fly naked in the air, just like fish in the sea.
Venus is assumed to be lifeless since it has such a hostile environment, so the moral implications of colonization are not of concern. Since climate change is continuing to make the Earth less habitable, the answer is to adapt colonists to exist on other worlds, including Venus (yes, there's mention in my story about humans being adapted for changes in Earth's climate, but the key to human survival is diversity of locations).
I want to introduce a previously unknown intelligence living in the atmosphere somewhere beneath. Relatively few altered Earth colonists might not affect the indigionus race since they effectively are designed to live at different atmospheric levels. Sort of like how say, if humans had colonized Earth in small numbers at first, they might not have significant effect on intelligent marine mammals.
I'm having a concern with the potential pros and cons of continuing the colonization efforts. For instance, as more colonists arrive and establish habitats higher in the atmosphere, would the light being blocked from the Sun have an effect. I'm proposing that my native Venusians absorb UV light as a food source and that the biology of my adapted humans does something similar, but higher in the atmosphere. Since the colonists and the indigenous beings eventually will be competing for the same resources, would the only solution be to abandon colonization efforts? After all, the colonists can't be returned to human form and can only exist above Venus.
What are some potential answers to the two "races" co-existing without adversely affecting each other and the environment?