That's not my functionality, but it's possible that I could be interfering with it. Please try to reproduce this with the main KoboTouch driver with calibre in debug mode. If you can reproduce it with the mainline driver,
submit a bug against calibre and include the debug log. If you can't, reproduce it again with my driver and submit a bug with the debug log. In either case, make sure to include whether you're using the old calibre database back end or the new back end. If you see "[newdb]" in the status bar you're using the new back end.
Please also remember that bookshelves are only handled on device connection. If you delete things in calibre the bookshelf changes will only happen the next time you connect the device. This is a limitation of Kobo devices, we can't do anything about it.