From this support request:
https://skyline.ms/announcements/home/support/thread.view?rowId=47889
If you do a "reimport" after adding new transitions to existing precursors with manually chosen peaks, then new transitions end up with peak areas that are null.
This happens because of this code in TransitionGroupDocNode.UpdateResults:
var results = nodeTran.HasResults ? nodeTran.Results[iResultOld] : default(ChromInfoList<TransitionChromInfo>);
if (results.IsEmpty)
resultsCalc.AddTransitionChromInfo(iTran, null);
else
resultsCalc.AddTransitionChromInfo(iTran, results.ToArray());