Skim stores the notes in the extended attributes of a file. A problem is that iCloud by default strips extended attributes, and therefore also the Skim notes. However with certain flags added to the attribute names iCloud preserve them. That is what syncable notes do.
The latest release wil be able to read the notes with these flags added. But it will not write them (yet), because it may exchange data with older versions of Skim, that cannot read this. You can set a hidden preference to have Skim write these more reliable notes. But be aware older versions won't be able to read them. We probably will make this option public in a later release, and perhaps make it the default. Christiaan
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