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Furthermore; how did the pods <span class="mu-i">know</span> to preserve the lives of the people at the time of their extinction, instead of having people from before or shortly after? How did it select for intelligence, and didn't simply grab any living creature of any species? The pods don't seem to be specially connected to the planet's species, there was no seeming sample granted of the race's DNA for it to draw from to find suitable candidates. In fact, the Life-Vaults were probably buried millions of years before those species ever even evolved.
But you have a more pressing affair.
The Life Pods that spit out the genocided members of the Vetucker and Swall races are not static. They are not one and done. The pods are continually producing more; perhaps as a method of repopulation after a mass extinction. But each pod is producing more of the same <span class="mu-i">individual</span>. Of the few scant million Swall and Vetuckers who have come back from their extinctions, there are now identical clones being produced by the life pods, given the same memories and biological state as the survivor was when first ejected from the pod.
<span class="mu-g">"...Why does the future have so many clones?"</span>
Currently, the Hegemony is <span class="mu-s">99% Jaxtian</span> in its demographic and will likely stay that way for a very long time. However, the life pods are producing new Vetucker and Swall clones at an astonishing rate, only taking a few weeks to spit out another cloned holocaust survivor. What this means is that the efforts to repopulate the empire with Vetucker and Swall could actually be helped by simply leaving the life vaults as they are. But that means there are multiple Vetucker and Swall clones running around; millions upon millions of copies, to which some of the aliens find distressing.
Of course, with the newfound massive expansion of the Hegemony's territory in space, your mega structure product, and the many many generations it would take to regrow the Vetuck and Swall to their original population; this strange quirk of the life pods may be a benefit. On top of this, your scientists and behavioral psychologists are loving seeing how the subtle changes in environment and their prospects in the Hegemony is affecting otherwise identical genetic duplicates. It's great fuel for your AI system's algorithms, especially for the new converts to the Hegemony who you need to build more data on. But at the same time, the aliens may feel a bit like replaceable products on an assembly line then unique individuals...
>Turn off the Life-Pods from producing more clones
>Study the socioeconomic impact of the clones in the wider Hegemony
>Continue producing cloned survivors to increase the Swall and Vetucker populations to healthy numbers