I’ve had something like this kind of problem in the past when transferring 
annotated files between computers or emailing them to myself.  What solves it 
for me is to send the files as compressed zip files .

> From: Nicole Busch [mailto:[email protected]]
> Sent: 28 September 2014 02:26:10 BST
> To: [email protected]; For general discussion about using Skim
> Subject: Re: [Skim-app-users] "convert notes"
> 
> Yes sorry, I open the work (that was scanned and saved as a pdf) using Skim, 
> I make notes, and then export.  When I open them all that can be seen are the 
> circles or lines I have made but not the text notes.  I then have to click on 
> "convert notes" to have the notes show up.  I was wondering if anyone else 
> was having problems but it doesn't seem to be the case.  I will keep playing 
> around and trying things. 
> Thanks!
> 
> On Sat, Sep 27, 2014 at 5:04 PM, Dr Eberhard W Lisse <[email protected]> wrote:
> That's not what she means,
> 
> She annotates a scanned PDF, and it works not all the time, unpredictably.
> 
> el
> 
> On 2014-09-28, 00:36 , Christiaan Hofman wrote:
> >
> > On Sep 28, 2014, at 0:02, Nicole Busch wrote:
> >
> >> Hi, the students are handwriting on an assignment and then scanning
> >> the assignment to a pdf file and emailing them, I just don't
> >> understand why they don't all need to be converted or all don't show
> >> the embedded notes when exported.  I haven't tried printing to pdf, I
> >> will try that thanks!
> >>
> >
> > If they are scanned from handwritten "notes", than they are not notes in
> > any way, neither Skim notes nor PDF annotations, but they're really part
> > of the (scanned) PDF. So there's nothing conversion can get out of them.
> >
> > Christiaan
> >
> >> On Sat, Sep 27, 2014 at 2:54 AM, Christiaan Hofman <[email protected]
> >> <mailto:[email protected]>> wrote:
> >>
> >>
> >>     On Sep 27, 2014, at 7:09, Nicole Busch wrote:
> >>
> >>>     Hi,
> >>>     I use Skim to mark assignments that student submit online.  I
> >>>     have found that every so often I will mark an assignment, export
> >>>     it with embedded notes, and save it.  And when the student or I
> >>>     look at it we can't see the notes.  I have learned that in these
> >>>     cases I have to go back in and click "convert notes", re export,
> >>>     re save, and re upload to the student.  I am finding this is
> >>>     happening a lot lately.  It is starting to create some problems
> >>>     for me at work as it looks like I am not marking assignments.  Is
> >>>     there any way of either knowing which assignments (they are
> >>>     usually scans) will require this, or is there any way to get rid
> >>>     of this problem?
> >>>     Thanks!
> >>>     Nicole
> >>
> >>     I can't think of anything you can do about this. I gather the
> >>     student(s) don't use Skim, but some other PDF reader? If you
> >>     really need to switch a lot between embedded and Skim notes, I
> >>     wonder if Skim is really the tool for you.
> >>
> >>     Christiaan
> [...]
> --
> Dr. Eberhard W. Lisse  \        / Obstetrician & Gynaecologist (Saar)
> [email protected]            / *     |   Telephone: +264 81 124 6733 (cell)
> PO Box 8421             \     /
> Bachbrecht, Namibia     ;____/
> 
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