On Apr 25, 2012, at 13:03, Alan Harper wrote:

> Now that we have found who is the culprit, can you give me any idea of what 
> the bug really is

Nope.  Apple doesn't have a particularly good track record with respect to 
preserving PDF features intact when saving.  This is part of the reason Skim 
uses extended attributes.  You should file a bug report with Apple at 
<http://bugreport.apple.com>, but you probably won't care by the time it gets 
fixed.

> and if there is a way to work around it?

Save using one of Skim's non-destructive methods (extended attributes, which is 
the default, or pdfd bundles).  Neither of these will allow you to see your 
notes in Acrobat or other PDF readers, though.

I guess you could also try re-distilling the corrupted PDF with Acrobat or 
Ghostscript.  PStill is another option, but the Mac OS X version is really 
ancient and will lose PDF bookmarks (IIRC).

-- 
Adam


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