I'm just wondering how to convert Blu-Ray source files to another format such as, preferably, MKV?
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You could mux the .m2ts files together with mkvtoolnix GUI. MakeMKV is also free while in beta. The beta key is posted on their forums. MakeMKV you will just have to open the "index.bdmv" file from your Blu-ray folder and then it will just open it like it's a Blu-ray disc and output whatever video, audio or subtitle tracks you select.