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When you encode with Handbrake let the default VFR or you use Constant Framerate - Same as source?
Your source was already VFR?
When there are VFR involved is easy lose the audio sync when recode.
If source and encode are CFR (the full source have the same frames than the fragments) when you add the full audio to the full video recode must be in sync.
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BeHappy, AviSynth audio transcoder.
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