I downloaded a BDMV folder that should be a copy of a six disk box set. All the files seem to be numbered with .#.ext in them. All the files came in one root folder.
Once I organized this into a streams/playlist/clip/meta folders by file type and feed it into makemkv I can only see disk one.
There are also 12 index files called index, index.1 index.2 and so on.
How do I rearrange this to see disk 2-6?
Yeah that's probably right since each disc likely had the same named files in them (e.g. same name .m2ts files).
You're right, that makes no sense either :/
Personally I would consider this corrupted data & just move on / try to find another source for that content. Otherwise seems like you're going to be spending a fair amount of time trying to reverse engineer whatever happened here.
What is your final goal? Are you just trying to mux the .m2ts stream files into .mkv containers? I suspect you can work with the .m2ts files directly & feed that right into ffmpeg or makemkv for the same results (granted not sure if you'll lose anything extra like subtitles). The trick is figuring out which .m2ts is which episode or whatever, you already have enough clues to figure out which .m2ts files are being referenced.
Also fun fact: Most media players can play .m2ts directly without needing to mux into a .mkv container first. I usually just hardlink the actual .m2ts files & rename them as needed for Kodi or whatever e.g. "blahblah.s01e01.m2ts"