Now I have had 2.1.3 installed for a week. The first days there was no sync at all but then reading plans and favourites get synced. Some of my notefiles is downloaded to the IPhone and the note icons shows up in the text but non of my highlights. If I create a new notefile on the desktop it is not synced to the iPhone. I think my downloaded note files is synced in previous versions of the app.
I can create an highlight on the iPhone and after a while it shows up on the desktop but non of my higlights from the desktop is viewable on the iPhone. In the "View Settings" I have set "Notes and Highlights" to "On". (This is how it worked in 2.0.2 as well).
Is the sync engine working to the rest of you?