After the usual 10s delay, Skim opened and showed me the corresponding section, *without* the part of the text I just commented out *without* having typeset the document before.
Oliver, this is limitation of Skim. The problem, insofar as I understand it, is that latex writes the pdf incrementally and not all at once. Skim uses some kind of heuristic to figure out when latex is done typesetting. Sometimes this goes wrong, if it takes a long time, and so some of your changes may not be displayed.
Best, Mark