This issue is addressed in Final Cut Pro X 10.0.5, Motion 5.0.4, and Compressor 4.0.4.
Final Cut Pro X, Motion 5, Compressor 4: HTTP Live Streaming segments are not replaced
When resubmitting an HTTP Live Streaming job that has already successfully been processed, the resulting .mp4 files are overwritten. However, the newer HTTP Live Streaming segment (.ts) files are created in addition to the already existing files.
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