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When I ripped a Ballet Video named E3XCELSIOR, I noticed two error messages about calculated BUP offset not matching the ones in IFO headers (bold, italic, underlined).
I wonder what this error message means and what is the effect during playback.

Here is a copy of the error messages as well as other information:
MakeMKV v1.9.3 win(x64-release) started
Debug logging enabled, log will be saved as C:\Users\User/MakeMKV_log.txt
Using direct disc access mode
Calculated BUP offset for VTS #1 does not match one in IFO header.
Calculated BUP offset for VTS #2 does not match one in IFO header.
Title #1 was added (17 cell(s), 1:59:09)
Title #2 has length of 20 seconds which is less than minimum title length of 61 seconds and was therefore skipped
Title #3 has length of 15 seconds which is less than minimum title length of 61 seconds and was therefore skipped
Operation successfully completed
Saving 1 titles into directory G:/BALLET VIDEOS/EXCELSIOR
AV synchronization issues were found in file 'G:/BALLET VIDEOS/EXCELSIOR/title00.mkv' (title #1)
AV sync issue in stream 1 at 0:48:06.403 with duration of 76.666ms : audio gap was filled with silence

It means there was some funny business done with the directory structure, and that MakeMKV had to work around it. As long as you don't get a message about failing to save the file, the playback should be fine.