Good news everyone! It's far less stupid if you export in XML format. So, step by step:
- Select a video in iTunes and hit command-R to show the file
- Delete (or move) the version without "(HD)" in the name
- Go back to iTunes and choose File > Library > Export Playlist
(this will export, for example, your whole TV Shows section)
- Make sure the format is set to XML
- Delete the files from iTunes, but don't move them to the trash when it asks
- Choose File > Library > Import Playlist
and select the file you exported.
Still kind of a pain, but at least you shouldn't lose any metadata this way.