I haven't read the book that you referenced so therefore I can't comment either way.
Having started collecting when Civil War weapons were still in abundance & affordable (by todays standards) in the 60's, Parts were found to completely rebuild a weapon but with pistols & especially Colts, the parts were stamped with the serial number of the pistol. A rebuilt pistol would then have mixed numbers & to a collector, not as desirable. The cylinder had the last 4 digits of the serial number stamped on it. I have never seen cylinders W/O a serial number and the only exception is one with the number severely worn off but you most definitely can tell if a number has been worn off & a cylinder in the white (W/O serial #) would almost be impossible to have been obtained from the factory.
A conclusion one would come by is that if extra cylinders were manufactured for a pistol, somewhere along the line a collector would come up with an extra cylinder to match his pistol. Since people have been collecting Civil War weapons since early of the last century, there has never been mentioned that a collector has come up with 2 matching cylinders for a pistol.
My thinking is, if replacing a cylinder was in practice during the war, why would a cavalryman (Confederate Guerrillas in particular) weigh himself down with so many pistols when he could carry several loaded cylinders in saddlebags & not weigh himself and his horse down with so many pistols?
I guess as a collector, I find myself sometimes questioning some things I have read in history & think, how was that possible?
Having read books written by some of the Guerrillas that rode with Quantrill, Todd & Anderson, years after the war, They did have a tendency to stretch things a wee bit so I do take some statements from books with a grain of salt instead of taking it for the gospel truth
If an answer can be made to change my way of thinking, I do have n open mind.
I will have to read the book you mentioned & see what was mentioned to exchanging cylinders.
Anyway, an interesting thread.