The reason that you are not seeing all of the expected chromatograms for the molecule "Isoleucine" is that the name of that molecule used to be "Leucine" and then you renamed it.
Skyline used to have a problem that if you changed the name a molecule the chromatograms associated with that molecule would disappear.
In order to fix that behavior we made it so that Skyline would remember the old name of the molecule and, regardless of how you rename the molecule, the chromatograms would always be associated with the original name of the molecule.
This has unfortunately led to the problem that you are seeing now where the Isoleucine and Leucine molecules are trying to store their chromatograms in the same place in the .skyd file. This conflict would not be happening but for the fact that Isoleucine and Leucine also have the same mass as each other since the chromatograms in the .skyd file are indexed with a combination of the molecule name and its m/z.
I cannot think of a good way to work around this in Skyline.
One thing that you could do is open up the .sky file in a text editor such as Notepad and find and delete the following text:
chromatogram_target="#$#Leucine$C6H13NO2$"
(I have attached a copy of "Missing_transition.sky" which has that text deleted)
I will ask around and see if we can come up with a fix for this.
-- Nick
Missing_transition.sky.zip
aAA_5.raw