Christiaan-

I found the Hidden Preference that I think you are alluding to:

" Automatically Open a .skim File

Key
     SKReadMissingNotesFromSkimFileOption
Values
     -integer, 1=always, 0=never, -1=ask
Explanation
     When a PDF file does not have notes, but there is a separate 
.skim file with the same name as the PDF, Skim can automatically read 
the notes from that Skim file. By default it shows a dialog for 
confirmation, but you can also force to always or never read the 
notes from the .skim file without asking. "

However, when I use the command lines

defaults write -app Skim SKReadMissingNotesFromSkimFileOption -integer 1

or

defaults write -app Skim SKReadMissingNotesFromSkimFileOption 1

in Terminal, I don't see any change in behavior when I restart skim. 
In other words, an updated .skim file is not automatically opened in 
the pdf (which already has some notes saved in the EA of the pdf 
file).  An I doing something wrong here?  Am I expecting the wrong 
behavior?  In other words, does this option only work if the notes 
are completely missing from the pdf file itself?

Thanks,
Bill

At 1:36 PM -0400 9/25/08, Bill Mohler wrote:
>Is that hidden preference already documented on the Wiki?
>
>>Skim only looks at the file name, nothing more. By default, Skim asks
>>you to add the notes from a .skim file if the PDF has no Skim notes
>>and a .skim file with the same file name is found in the same folder
>>as the PDF. You can force change whether it does this, or does so
>>without asking, using a hidden preference.
>>
>>Christiaan
>>
>>On 25 Sep 2008, at 7:07 PM, Bill Mohler wrote:
>>
>>>   Is there a way to have Skim automatically open the .skim file
>>>   associated with a pdf when the pdf is opened?  I have the impression
>>>   that it does this by default on many occasions, but it does not seem
>>>   to be happening for files that are updated back and forth between my
>>>   two machines using FileShare.  In otherwords, an updated .skim file
>>>   is not automatically opened by Skim when I open a pdf after an
>>>   update.  I think this is more a Skim behavior issue than a FileShare
>>>   issue.
>>>
>>>   Thanks,
>>>   Bill
>>
>>
>>
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-- 
-----------------
William A. Mohler
Associate Professor
Dept. of Genetics and Developmental Biology
University of Connecticut Health Center
MC-3301
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