So if I understand it correctly, you previously used pre-prepared ISOs, right? So you never had to turn an MKV file into an ISO using a program like tsMuxeR?
SRT files are subtitles, so they’re optional unless you need to view them during the movie. The one huge MKV file (> 40 GB) is the only thing you need to make a Blu-Ray compatible ISO. The smaller MKV files are also optional.