Note appear to be iterated through in order of the splits in the file, so if you have splits and notes like:
Split A: Note 1
Split B: Note 2
Split F: Note 3
Split G: Note 4
then when you add more splits in the middle and don't go three menus deep to open SGL and do nothing but hit save, the notes wind up in the wrong places: C and D get notes 3 and 4, etc.