This is not the quick, easy method but the slow, hard method. The blu-ray may have hundreds of playlist (.mpls) files but only 15 or so stream (.m2ts) files make up the movie. The playlist file says in which order to play the stream files.
The playlist and stream files are available if you make decrypted disc backup in MakeMKV. The movie stream files are often 005##.m2ts while the other stream files are previews etc. Sorting these is easy if the blu-ray is cued up nearby. Pause the blu-ray movie just past the end of one stream and play the other stream files until one matches. Write down the correct stream file order in one column. Keep a running total of the stream times will help locate the change points in the blu-ray movie.
Don't search all the playlist files to find the right one, just edit one of the possible playlist files and save as a new playlist. I haven't found a playlist editor so resorted to a hexeditor to modify and save the new playlist file. The stream files play in sequence so write the order of .m2ts filenames from the sample file in a second column to see what changes are needed.
Find a sample playlist which has the first and last .m2ts files correct and make a copy. Open both in the hexeditor and copy an m2ts block (filename and all below upto the next filename) from the copy file. Highlight another block in the original file at the correct sequence position and paste. Eventually, the blocks will be in proper sequence in the original .mpls file. Now save the original file as 01000.mpls. The sample .mpls file and its copy are left untouched.
Open index.bdmv with MakeMKV and the bottom text should show 01000.mpls is identical to, say, 00533.mpls and was skipped. The 00533.mpls file is correct for this movie.
Edit:
1. Don't be intimidated by using a hexeditor. All the changes to the M2TS filenames are on the text side of the file display on the small .mpls file.
2. The backup blu-ray copy and created MKV should be on separate hard drives for the best speed.
Edit 2:
Added paragraph 4 as changing only the m2ts filenames in the mpls file will fail.