Join Date: Dec 2009
Location: San Francisco Bay Area
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it's down and dirty, but what not just use windows's search function? Assuming you have all your movies in the same format, such as MKV, just search for *.mkv from All Movies including all subfolders. The results should be in alphabetical order. From there, just look for the smaller file size, which should be lower resolution movies. Plus, it should give the file location in the status bar, which is a secondary indicator. Then it's just hit delete. It may be faster.
I know Plex, and I believe XMBC, will list every movie file. You'll just want setup your movie folder at the "HD Movies" and the other folder "nonHD" into the just one Movie section. When you go through, it should list both movies with the same metadata. But if you look at the details, one should show 720p/1080p and another for SD resolutions (480p). As long as you have it setup, you should be able to detele it from there; I think off the HD, not from the library. Plex has an option to hide a movie.
Personally, I would go with my first solution.