There is nothing we can do about this from Skim. This is purely a thing of
the converter. You should also realize that the page numbers in Skim aren't
really numbers, to which you can apply arithmetics. They are text, e.g. it
can be a, b, c.
I have been using Skim for a long time and it is just perfect. One
thing I noticed, especially for scanned scanned books, is that the
page numbers of the PDF and the page numbers of the book itself
mismatch. I wonder how people usually deal with this.
1. I could image set some kind of "offset" in
