Reporting back. I have (I think) resolved the issue.

At Jan's suggestion, I tried highlighting the same PDF file with Documents
by Readdle for iOS. I also added highlights with Adobe Acrobat for OS X,
and also with FoxIt Reader for OS X (Desktop). Then, running it through
Skim again (*File > Convert Notes...*). All the highlights made by
Documents, Acrobat, and FoxIt Reader Desktop get converted to notes as I
would expect. Only the highlights made by FoxIt MobilePDF fail to convert.

My conclusion: it's not a fonts issue, nor is it a problem with Skim.
Rather, the problem is that the highlight bounding boxes created by FoxIt
MobilePDF are too short. Looking closely, this is visible on the screen,
too.

Actually, what I would really like also is a way to perform this conversion
via the command line or some sort of code library. I.e., a highlighted PDF
is the input, and the output is XML that contains the text in the
annotations, page number, details like timestamp, etc.

Any ideas about doing that?

On Mon, Oct 29, 2018 at 10:52 PM Jan David Hauck <[email protected]>
wrote:

> I've had exactly this problem before (including the fact that italicized
> text gets converted correctly).
> (See here
> <https://sourceforge.net/p/skim-app/mailman/skim-app-users/thread/BCF49C1E-DAAD-4A0B-B424-43C299AADE82%40gmail.com/>
>  for
> original discussion on this list.)
>
> In my case the culprit were scanned PDFs that were OCR's using Adobe's
> clear scan mechanism and then annotated with Adobe Reader on the iPad.
>
> I've switched to using the Documents app from Readdle on the iPad, and
> those notes get converted without problems.
>
>
>
> On Mon, Oct 29, 2018 at 5:44 AM Christiaan Hofman <[email protected]>
> wrote:
>
>> Try to select some text and add a highlight in Skim or copy and paste the
>> text.
>>
>> Christiaan
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