Syncthing works okay for this. I've used it with Retroarch to sync content, save states and system BIOSes and what not successfully for a little over a year. The problem with using it is that when the LaunchBox Windows Desktop version exports to the same location it first deletes everything in that path and then exports, deleting the .stfolder that Syncthing uses to keep track of things and thus breaking it. You can still use it, but it's clunky and very easy to break. I can export to a temp folder, as I believe was intended by the default temp path, and then copy that over, but if you're exporting games from an existing system the XML metadata file will be overwritten and again you have to be conscious of the .stfolder/.stignore files/folders. The export process needs a lot of work, hence the beta status.
I would like to see the export process improved to where we can add content to an existing export. Being able to change the default export to something else would be nice and maybe an option to exclude certain files/folders from being overwritten/deleted in the export process.
I hope these things can take a little more priority because while I can see the way that it currently works for people exporting a bunch of content to a tablet or something, I think there are probably just as many if not more people like the OP and myself who want to cherry pick from our massive rom collections and add a game here or there without re-exporting everything again.