Thank you, Christiaan. Perhaps .skim notes are the best way to preserve 
editability, and searchability, and also future-proof my notes so that they 
will be accessible when everything I now know is different.

A

On Jan 22, 2013, at 13:37 , Christiaan Hofman wrote:

> Spotlight of PDFs is already done by Apple. This means that attached Skim 
> notes are not searchable through Spotlight, because Apple does not know about 
> that. When exported with embedded notes (i.e. flattened), they become part of 
> the PDF data, and the PDF importer may pick them up, though I am not sure 
> about that, as Apple won't tell us how it works. Whether embedded notes are 
> edited with Acrobat, Preview, or some other program that embeds the notes in 
> the PDF should not matter, it should be the same kind of data in the end, so 
> I have no idea why they would give different result. As for Skim, you can get 
> the notes indexed if you save as pdf bundle (PDFD), or when you save the 
> notes also externally in a .skim file (you can have that done automatically, 
> also handy as a backup of your notes.)
> 

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