I suppose there's a variety of reasons for this, but two possibilities
come to my mind, and both cannot be excluded so far

(1) You're using the wrong highlight tool in PDF Expert - the one that
does not actually highlight the text, but the one that basically works
like a real highlighter by allowing you to arbitrarily highlight
anything in any shape anywhere on the page. Then the note will not
have any text content because it is only associated with a position,
not any text.

(2) Your sample PDFs are affected by the lovely bug in PDFKit that
completely destroys the PDF encoding.

If you say "the note are perfectly visible with Preview", does that
mean that the "Highlight&Notes" pane
(http://moultriecreek.us/gazette/files/2012/08/Preview102-640x463.jpg)
actually shows the text content of the highlight when opening the PDF?
If yes, (1) and (2) can be exluded.

If it is (2), viewing the "Highlight&Notes" pane will display a bunch
of aliens (honestly:
http://apple.stackexchange.com/questions/61437/preview-copies-aliens-how-to-change-the-encoding-make-it-work).
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On Wed, Jun 4, 2014 at 12:29 PM, Nicola Carboni <[email protected]> wrote:
> Hi everyone,
> I would like to export my highlights in a text file, and I have some problems 
> doing so.
> I usually highlight my papers on the iPad (PDF Expert), then sync with 
> dropbox. I then open them with Skim, convert the notes, and then export them 
> in a txt file. But the output is the following one:
>
> * Highlight, page 2
> * Highlight, page 2
> * Highlight, page 3
>
> Instead of the actual text!
> I tried with different PDF and I have the same problem.
> What I am doing wrong?
>
> Thanks in advance!
>
> Nicola
>
> P.s. the note are perfectly visible with Preview
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