I have imported a PDF into MarginNote on my Mac, it synchronised to my iPad literally in a few moments. On my iPad I opened it, added a few annotations and then closed it. 2 hours later the updates have not copied across to my Mac.
I’ve read a few threads about sync issues and looked in the MarginNote 3 folder in iCloud but that just has the original PDF, not the marked up version.
The marked up (annotated) version only appears in MN3 on my iPad.
At present I am using a 14 day trial of MN3 on my Mac as I have not upgraded from MN2 until I experience it actually working.