To quote Keith:
If you ever happen to look under the hood of a Scrivener project, you’ll notice that the files there are all a flat list stored in one folder on the hard drive; their hierarchical representation within the program is done by xml. So it’s not really just a matter of copying the folder structure from one place to another, since the folder structure doesn’t really exist in Scrivener.
Anyway, a couple things you might try to alleviate your problem a bit, if you aren’t already doing them: 1) Turn on file numbering in the sync options, to keep your flat list in the proper order when you’re viewing it outside Scrivener (rather than defaulting to alphabetical). 2) If your work style permits, sync only a selection of notes at a time. A quick way to do this would be to create a “For Syncing” collection and then just drag into that what you need to take with you.