I have UHD Blu-ray movie Cleopatra (1963) in my library which has two BDMV folders from disc1 and disc2. What is the best way to scrape it? Should I convert it to MKV then put two in the same folder?
As you said, convert to mkv files, then use MKVToolNix and join the two files together to create a single movie file... https://mkvtoolnix.download/downloads.html
(I have done that for my Lord of the Rings movies)