Tell your workflow. It is better to get that straight in the first place instead of trying to fix that up afterwards.
Still you can rip your Blu-ray, decode that and diff the 2 streams, source and encode.
ShowTheDifference is an old one, and StainlessS has written nice scripts to achieve that in greater detail and ease of work.
Frame-accurate source filters are a must, you may use Atak_Snipera's tool for evaluation of frame-accuracy of a given filter.
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"To bypass shortcuts and find suffering...is called QUALity" (Die toten Augen von Friedrichshain)
"Data reduction ? Yep, Sir. We're that issue working on. Synce invntoin uf lingöage..."
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