Small factoid: In DOI, Patsy made a point of writing that John is very squeamish at the sight of blood. Conveniently, JonBenet's killer made sure that John was spared the sight of JonBenet's blood.
Fact to note: While the crotch of the underwear had blood stains, the crotch of the longjohns did not, indicating the longjohns were separated by some distance from the underwear at the time the blood was deposited, even while both were in contact with JonBenet's body. Supplemental fact: the blood on the underwear had left no equivalent stains or dried blood on JonBenet's labia where, by any reasonable standard of evidence, blood should have been left. Blood cannot leak out of a vagina onto underwear without passing across both the labia majora and labia minora.
Fact: The CBI found bloodstains belonging to JonBenet on her nightgown, her shirt and the blanket. Supplemental fact: It is impossible for JonBenet to have bled onto her shirt, the blanket and the nightgown from her vagina unless all these items were shoved up her crotch at some point.
Theory: The person who assaulted JonBenet did not realize she would bleed as much as she did. I will go with the premise BlueCrab presents that JonBenet was not wearing the size 12 panties at the time of assault. I theorize that JonBenet was assaulted and began to bleed. The killer carried JonBenet's own blood from, let us say, her hands to JonBenet's shirt, the nightgown and the blanket (and as I recall a small smear of blood was found on JonBenet's leg), all in a short time but in such small amounts that the volume of blood on shirt, nightgown and blanket was not easily detectable. The volume of blood on the underwear being worn was, however, obvious. To spare John the sight of blood on his daughter's crotch, the killer removed what underwear were being worn and replaced them with the size 12s. It was only upon seeing that JonBenet's body continued to leak blood (not actively bleed as a living person would, but leak as dead bodies are capable of), that the killer then took one last bit of effort to wipe JonBenet's labia clean and then pull the size 12s up once and for all.
Bonus question: I would like to know if JonBenet owned any dark underwear. It is not impossible. If that were true, the dark fibers on her crotch may represent her very own underwear having been used to wipe her clean of blood, with said underwear being tossed into one of, let us also say, 40 purses in the house, none of which would be an immediate target for a police search for evidence. And if that purse were removed from the house by a grieving mother or, days later, her helpful sister, who would know?