I had been reading several papers and highlighting important points, pressing Command-S every so often to save my notes.
But when I opened them back, BAM! All my highlights were lost.
It turns out that I have to do
File > Export... then choose to save the PDF with embedded notes. Add to that, I cannot press Command-S to save with embedded notes on the same file.
That's totally counterintuitive, takes too many mouse movements and keystrokes, breaks my train of thought, and just disheartening.
How can I make Skim save over the PDF with my notes included, simply by pressing Command-S by default? It was the default behavior until recently. It turns out they changed it in Skim 1.3.22