From this support request:
The "Permute Isotope Distributions" menu item was used with the "Complete" option to get all of the permutations of the heavy label.
Some of the precursors ended up with the same precursor m/z, but different transitions.
Those precursors would be written to the .skyd file as separate ChromGroupHeaderInfo's. When loading chromatograms, only the first ChromGroupHeaderInfo would be returned, so some of the precursors would end up missing transitions.
I think the fix might involve writing a merged ChromGroupHeaderInfo to the .skyd file.
The fix for this might also help the scenario in this pull request where multiple molecules had the same TextId.