Download the script skimbulk (linked on the Wiki). Put it, say, on your Desktop. Open Terminal.app, and type chmod a+x Desktop/skimbulk and hit Enter, to make it executable. Now in Terminal.app type something like Desktop/skimbulk get path/to/folder, where path/to/folder is the path to the folder containing PDFs that may have Skim notes, starting from your Home folder (a path is a series of containing folder names connected by /, starting from your Home folder). This should add .skim files for every...
implement setString: for PDFAnnotation of type Widget properly
Annotations are pixellated
duplicate of #1617
The bubbles also remain when you reopen? That means that the text should be really cleared, rather than just be an empty string. Unfortunately, that is not possible with the current release, and also I saw that clearing the text in the table does not work. In the next release both will be possible though.
I have put up another test version at the same link, this one to see if we can fix the low resolution drawing. The implementation is not complete, in particular AppleScript support is not complete, though most other functions should work.
fix method name
allow setting missing value for text, user name, and interior color of notes in AppleScript