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Does the frame rate vary all over the place or is it a combination of film and video, or that sort of thing. If the answer is yes, can you easily tell which section is which? If the answer is yes, you could go through the video and note the start and end frame numbers for each video section, or each film section, then make a timecodes file to match. A basic timecodes file looks like this:
# timecode format v1
Assume 59.940060
0, 3539, 23.976024
3540, 3699, 23.976024
5998, 6342, 23.976024
19263, 20258, 23.976024
22887, 23268, 23.976024
x264 still seems to need
# timecode format v1
as the first line when being fed a timecodes file for VFR encoding, but for muxing I vaguely remember MKVToolNix switched to
# timestamp format v1
Although it might still accept either.
By the way. MKVCleaver and gMKVExtractGUI both tend to make extracting stuff from MKVs a fair bit less painful.
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