This part is off-topic: I’m troubleshooting a problem I’m having transferring Skim-annotated docs between machines (using Finder, PathFinder, or ChronoSync). The notes disappear because the extended attributes are getting stripped off someplace in the process. I’m convinced this used to work, but now it doesn’t. So it goes. As a workaround I’ve preferenced Skim to “automatically save Skim notes backups”, which causes Skim to put the notes in a sidebar file, that it imports with the PDF if it finds such. So far so good.
For DTPO the question is: I don’t think using the sidebar-file approach should cause any functional loss. Other than the annoyance of having to have Skim reassociate notes with a PDF by opening each file once. This is needed before the annotations are visible in DTPO.
Second DTPO question: I haven’t used DTPO for annotation much, until the feature settles down in the betas. Is there a risk that annotations created with PDFKit in DTPO are also stored in EAs and will get stripped too?