Emby doesn't respect folder location like 4.5.4.0
4.6.2.0 (LATEST)
4.5.4.0 (OLD)
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4.5.4.0 (OLD) [CORRECT]
4.6.2.0 (LATEST) [WRONG]
DUPLICATE PROBLEMS (4.6.2.0)
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FOLDER STRUCTURE
Season
That's also okay, but for your "A Computer Murder Case" example it should be <season>1</season> and <episode>43</episode> then.