Sometimes the most obvious evidence is the most damning..
That we've all known this whole time, but maybe slightly glossed over due to the exorbitant amount of information in this case.
For those of you that have kids... you find a ransom note your child has been kidnapped. Is there a room in your house you just "wouldn't check" in 3.2 seconds in this situation. There's no "around the corner out of the way" basement room that wouldnt have been searched within minutes for me. If the room was locked when I came across it, I'd be even more focused on getting into it, and wouldn't need to go back upstairs and wait until someone else suggests that maybe I go look for my kid again.
John just assumed she was gone, because uh..... the note said she was, so... John one of the most logical spoken high IQ type of people... just, didn't even bother checking the house after reading a ransom note.
John..... AND Patsy... just.... DIDN'T check the now locked wine cellar.
The second time Fleet and John go looking, they return within 5 minutes with Jon Benet.
Ain't. No. Way.
This isn't an implication of m*rder, but one of knowledge.