You are more or less correct on stem cells. They are cells that have DNA but have not yet begun producing specialized proteins needed to work as a part of the body. They just kind of sit there until they are called upon. Everyone has them, not just newborns. Adults have them in muscles and we currently have the technology to revert skin cells back to this helpful building block.
If Alponians are like stem cells, why are you bothering with a body in the first place? Kill them and let the alponians rebuild from the ground up.
Also, you still don't understand it. You can't instantly decompose every protein in the body. Let's say you manage to decompose all of protein x in the body. That would release enough of the amino acids contained in it to kill you. Triptophan for instance is a sedative. Enough will kill you.
The other thing is that these enzymes would have to be antibodies. Not just any antibodies, but cell sized mega antibodies. Injecting someone with enough of these to actually break down every cell would clog their blood and kill them before you ever started the process.
So, yeah... The Alponian idea, while creative, is not possible. I know you'll say, "but they are more advanced!" and I have two responses:
1. Simple anatomics and chemistry make their usage impossible without killing the host at some point along the line, be it the injection, the bonding, the decomposition, DNA change, or end result. The subject will die.
2. If they are so advanced, why bother with alponians if you can build a new Vasari from the ground up in a matter of hours rather than waiting at minimum a few weeks for the bugs to take control?
Also, we can assume that since the capitals carry so many nanites that they have vast bays containing seas of nanites. Just take the nanites in one bay, feed them some raw materials like carbon, hydrogen, oxygen, nitrogen, and iron and you will soon see the sea of nanites creating a Vasari army in the course of a few hours. If you want to quick-crew a capital, what better way than to build one?
Oh, and for further evidence of the nanite contruction idea, I did some math. First I assumed that terran planets are earth sized. Next, I checked the diameter. Its about 12000 units. When I went and checked the size of the earth, its diameter is about 12000 kilometers. This means that a unit in sins is more or less a kilometer.
From there, I did some more with the radius of repair cloud. I put it down as covering a few thousand cubic kiloms before. I was severely mistaken in my estimation. Try something more along the lines of 1.4 TRILLION cubic kilometers! Do you realize how many nanites that would require? The Skirantra would have to practically be a ball of nanites!
The same general concept can be applied to the Kortul that has VN which covers 113 billion cubic kiloms in nanites. Or the Jarrasul with its nanite bomb. The Vasari are in no short supply of nanites.
I also checked the math and capitals are actually thousands of kilometers long and hundreds of kiloms wide. They aren't exactly small...
So really your basis for arguing for alponians has been, they're cool. Scientifically, alponians won't work. Economically, nanites are cheaper, faster, and more reliable. All you have been doing is using things that you think you know about the body to try to justify it. Trust me, you can't just swap out the proteins and DNA. Really all you'd be doing is building a new Vasari anyways. Why waste your time with an old subject? You support you idea on invalid information and have made no attempt at shooting mine down. I appreciate a challenge in a debate, but you seem to have given up hope of winning this as you seem to be making last-ditch efforts to save and idea that belongs in Sinners, but not here.
Once again, I love your story, but Alponians just aren't practical. Every step of the way they are ineffective (or worthless if counting the fact that they would kill people) compared to alternatives.