The dialog you get when you open the FLA in CS6 is that new features may not be available in CS6 so you should save it to a new file to avoid corruption. There's no "save down" from CC to CS6 (yet). So opening the file in CS6 isn't advisable in the first place.
That said, library items are supported between them both so to your point, yes, I get the same exact behavior. A single symbol named ">" in CC produces 2 library items in CS6 named ">" and ">", and the original item is lost. Although I'm not sure where I'd classify this issue being you shouldn't be opening a newer version file from an older version of the application. I did also try XFL, same issue. If they decide to create a save-down to CS6 and this still exists, I'd consider it a bug.
As for a fix, I think about the only thing that comes to mind is identify the characters causing issues and run a JSFL in CC to rename the library item temporarily to something you know will work fine. Then once back in CS6, run the JSFL opposite to convert them back to what you want. e.g. "this > that" to "this XYZ that" in CC, then "this XYZ that" to "this > that" in CS6. Shouldn't be too hard to map as long as the replacement is unique.