Thanks, Christiaan. Actually, exporting as embedded notes does work.
All the documents I had previously exported/embedded display all notes
fine in whatever OS or app. But exporting now doesn't make them
visible again - they needed to have been exported on OSX Yosemite.

I for one would be extremely grateful if you could figure out some
kind of workaround even though it's Apple's fault, not yours!

> On Dec 28, 2015, at 16:23, Caleb Anderson Day <elcalebo@...> wrote:
>
> Hi,
>
> I'm having the same problem as everyone else who's upgraded to El Capitan: 
> Freehand notes aren't visible anymore. I had a whole lot of important 
> freehand notes on old documents that I (foolishly) didn't export as embedded 
> notes before upgrading to El Capitan.

I doubt that works, because the problem is in the system code, so they
should apply to both forms.

> Looking at the Notes pane, I see that all the freehand notes are still 
> technically there; I just can't see them (or sometimes I see a few of them 
> but in the wrong place). So my question is: Does anyone know of another way 
> to 'get those notes back' or make them visible in any way without downgrading 
> back to the previous version of OS X? (Or has anyone tried downgrading OS X, 
> and if so, did it work?)
>
> Cheers,
> - Caleb

You can’t really, because, as I said, the bug really is in the system,
not in Skim, we’re not involved in drawing these notes.

Christiaan
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