Before merging, export the skim notes for the two files to separate files (File 
> Export…). After merging, read them in (File > Read Notes…), make sure you 
uncheck "Replace existing notes" the second time).

Christiaan

On Aug 10, 2010, at 9:04, Carl Lee wrote:

> Hi everyone (developers too?),
> 
> I have two Skim-annotated PDFs (sources 1 and 2) which I want to merge into 
> one PDF in that order (I use CombinePDFs to do the merging since Skim cannot 
> do this for me).  Problem is, when I do this, the annotations for both source 
> PDFs are gone in the merged PDF.
> 
> Q: Is there a way to *keep* the annotations after merging?
> 
> If there is no elegant solution, here's a kludge that I hope to carry to 
> completion:
> I have made some progress in that I *can* extract my annotations when I 
> export as "Skim Notes" and save them onto the merged PDF by using "File > 
> Read Notes...", but the page numbers for my annotations in the merged PDF are 
> the same as they were in source---so that source 2 annotations are not in the 
> correct location in the merged PDF.  What I want to do is "shift" ALL the 
> page numbers of source 2's annotations by an integer of my choosing (i.e. so 
> that they correctly correspond to the "new" page numbers where source 2 
> resides in the merged PDF) 
> 
> Please let me know if you have any ideas to make this work---this would be 
> great as I often find myself OCR scanning books one chapter at a time just so 
> I can annotate them in Skim!
> 
> Thanks!
> 
> -Bill

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