For a while now, iTunes has supported the concept of "HD+SD" files. Instead of having two separate files, one for the SD version and another for the HD version of a movie or TV show, iTunes can "bundle" both versions under one single file entry, which is labeled as "HD+SD", and iTunes automatically chooses the "right" version of the file to use for a given situation (e.g. use the HD version when streaming to my Apple TV, and use the SD version when syncing to my 16 GB iPad mini because I have "Prefer standard definition videos" checked in the sync settings). Here is a video describing this feature and how to use it.
I am using HandBrake to do the encodes, using the "Devices -> Universal" preset for the SD encode, and the "Devices -> Apple TV 3" preset for the SD encode, and am using IDentify 2 to do the metadata taqging. The problem comes when I attempt to add these files into iTunes.
In previous versions of iTunes this process was pretty straightforward: assuming that the HD+SD encodes are properly tagged with the same cnID (which mine definitely are, I checked), just select both the SD and HD encode in Finder, and drag+drop them onto iTunes, and it will automatically create an HD+SD entry for that movie/TV show/whatever.
Unfortunately I can't seem to get this to work in iTunes 11. If I drag both the HD and SD encodes onto iTunes, it results in only one of them getting copied. (seems to be random, sometimes it's the SD version and sometimes it's the HD version) If I then try and drag the other file in, it does not copy the file in nor does it create the HD+SD file entry.
iTunes 11 definitely still supports HD+SD files, as the ones that I added in previous versions of iTunes still work fine. I just can't seem to figure out how to add these HD+SD files in iTunes 11, because the way I've been doing it up till now no longer appears to work.