Interesting thing you've uncovered there. I wonder if it could be considered a bug?

For reference, the thing that I think is a bug was 4a. 4b is "by design" behavior as described here.

A way around it, in your case, could have been to do it in two stages:

- Move the one track out of that folder, then synch.
- Go back in and delete the larger playlist with the "delete all tracks" checkbox checked. Then synch again.

2.0 is pretty much feature-frozen at this point, but maybe this is something that can be looked at for 3.0?