Emailing a PDF file loses notes or highlights

Notes and highlights you add to a PDF document are not saved in the PDF data, but are added to the file as extended attributes. Those are usually lost when you email the file.

There are several ways to preserve the notes. Some compression methods preserve extended attributes. Apple’s Create Archive unfortunately does not preserve them. You should compress and expand to test whether they are saved. You can also create a disk image to wrap the PDF file. Compression using tar and gzip also preserves the notes.

You can also save the notes to a separate .skim file. The receiver of the email can later add the notes to the PDF.

And lastly, you can save the PDF and notes in a PDF bundle, that wraps the PDF and the notes together.

To save the notes to a separate file:

Choose File > Export….
Select "Skim Notes" from the File Format popup, choose a location to save the notes to, and press OK.

To add notes from a separate .skim notes file to a PDF file:

Open the PDF file.
Choose File > Read Notes…, and choose the .skim file that holds the notes.

To create an archive of the PDF document:

Make sure you have saved the PDF file with the notes.
Choose File > Save Archive …, choose a location to save the archive to, and press OK.

To create a disk image of the PDF document:

Make sure you have saved the PDF file with the notes.
Choose File > Save Disk Image …, choose a location to save the disk image to, and press OK.

To save the PDF and notes to a bundle:

Choose File > Export….
Select "PDF Bundle" from the File Format popup, choose a location to save the bundle to, and press OK.

It is important that the notes file is associated to the PDF file. Therefore it is best to choose the same file name for the .pdf file and the .skim file. In that case, Skim will automatically offer to add the notes from the notes file when you open the PDF file.