After restoring, HD iTunes "Lost" files lost! SD still there...

I recently had a Mac problem meaning I had to move files to an external drive. I did so - at the folder level, not file by file. I didn't check - I didn't have any reason to - but now I see that since I did the HD versions are gone. The HD-SD icon is still in iTunes but only file in ~/Music/iTunes/iTunes Music/LOST is the SD one for:
01 LOST Starter Kit.m4v
02 Because You Left.m4v
03 The Lie.m4v
03 The Lie.m4v
05 The Little Prince.m4v
06 This Place Is Death.m4v
07 316.m4v
From 08 The Life and Death of Jeremy Bentham (HD).m4v on - probably, after everything was back to normal - I have both. I am mystified as to what happened. I most certainly did not "exclude" the HD files, and clearly something happened as I have valid SD files. I see an Ars Technica article about HD files being deleted but I don't know if the circumstances are the same. I back up my music files to Time Capsule but not video, but I did back up to an external drive and as I say I have something. What might have happened? The files are not the end of the world - I have watched them - though I would like them back as I did pay for them. I am however much more concerned to understand what has happened as it really does seem like the files have disappeared, not been deleted through some user error / idiocy! Many thanks!