This was reported on the support board:
The key XML element that BlibBuild is failing to make sense of is:
<aa type="S" at="24" modified="44.00846" pm="M" />
As an initial fix, I think we need to just change the peptide to replace the S at 24 to M.
A more complete fix would preserve the point mutation information somehow in a way that would allow Skyline to make a correct protein assignment based on the original peptide sequence.