Trying to rebuild this my first time I took all files appended with .1 and placed them into a BDMV folder with the correct folder structure and index files. I then did the same for all the .2 files into another DBMV folder and so on. I then removed the appended numbers to these files.
This left me with 12 disk folders, though I could not get makemkv open any of these.
What I think I may have been missing (which I will give a shot tomorrow) was copying over the content that did not have a appended number originally into both these folders skipping any files with the same name.