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
No, your metadata is confused, regardless of what Emby version you run. You should correct it to represent exactly what you want and stop sending Emby conflicting information.