Dolby TrueHD is a lossless format. Generally it includes a 'lossy' core; this is 'regular' AC-3 5.1 surround sound.
DTS-HD Master Audio functions in a similar way with a lossy core of regular DTS 5.1 audio.
I'd probably keep both of them.
What is the stereo track? It might be a commentary track. It might be
descriptive audio. It might be a stereo mix of the main audio track. If you make a decrypted backup of a disc before making .mkv files, you can play the associated .m2ts file(s) in the /BDMV/STREAM/ folder for a particular title (see the segment map line in the info box on the right) and check. Or, you can make a .mkv from the backup, check the output, and adjust. Making .mkv files from decrypted backups goes as fast as your computer's storage allows.