The Moon Colony Hypothesis
The breeders may not have died. Some may simply have left.

The Moon Colony Hypothesis
The breeders may not have died. Some may simply have left.
If the avian civilisation had biotechnology advanced enough to engineer apes, it is reasonable to assume it also understood one basic principle:
do not keep your entire civilisation on one planet.
When the ape revolt began, some breeders may have escaped to the Moon.
Not because the Moon is comfortable.
Because it is defensible.
Visible from Earth. Difficult for primitive apes to reach. Perfect for preserving archives, genetic material and command structures.
Why the Moon?
Humans treat the Moon as empty because humans arrived there late and found no obvious cities.
This proves surprisingly little.
A species capable of designing living organisms would not necessarily build lunar bases like apes build airports.
It might build underground.
It might build biologically.
It might build things we would mistake for geology.
Conveniently, geology cannot testify.
The Intelligence Problem
A functioning lunar evacuation would require planning across generations.
Resource management.
Strategic patience.
Civilisational continuity.
That is already a higher standard of cognition than some modern ape leadership routinely demonstrates.
No IQ test is necessary.
One group escaped planetary collapse and maintained a hidden refuge.
The other group struggles with microphones.
They May Still Be There
If even a small breeder population survived, then humanity did not inherit an empty planet.
We inherited a monitored one.
The Moon is not necessarily a graveyard.
It may be an observation post.
The breeders did not vanish. They took the high ground.