For user files, notes and prayer requests specifically, Logos should provide the ability to determine what's synch'd and what's not. I would actually consider this request critical in terms of privacy and copyright protection, of little to no cost in terms of support, and little to no cost in terms of actually coding and supporting such a feature.
It would be nice if this were per note or prayer list--IE, on the options for that particular note or prayer list, there was a "synchronize this" option. Then you could select some files with "private" data to remain local, and others to be synchronized. I think Logos stores all your notes in a single database file right now (I can't seem to find a way to give someone my notes for a particular stretch of Scripture at the moment), so that might not be possible--it might need to be an all or nothing affair. But the stretch goal would be for individual notes file synchronization.
Russ