Suggestion for saving some time.
I'm working on rebuilding a Blu-ray from its contents (long story). The main video is 30 GB. When importing the files, BD-RB separates the streams from the MKV files and then remuxes those into the M2TS files. Those files are then deleted.
Then, when the backup is started, the M2TS files are separated into the individual files so that the video can be recoded. Why? Keep the files from the first demuxing. Rename/move those files to the new work area for recoding and remuxing. With a 30 GB file, it takes a while to demux and doing it twice, IMHO, is a waste of time. Only do it once.
Like I said, a suggestion.
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