Currently MakeMKV does a fantastic job of perfectly preserving 99% of video content from DVDs with one notable exception: CEA-608 Closed Captions embedded in the MPEG-2 video stream itself. MakeMKV does use CCExtractor to convert such captions to SRT subtitles, but this conversion is not lossless; specifically, positioning information is lost as part of the conversion. Additionally, these captions are not present in the MPEG-2 video data found in the final MKV produced by the program, apparently stripped out during some portion of the processing. This means there is no way to do a 1:1 restoration of CEA-608 Closed Captions in content backed up with MakeMKV.
To address this I would like to suggest that MakeMKV's default processing be altered to leave the CEA-608 Closed Captions in the user data in MPEG-2 video streams. Failing that, CCExtractor is capable of outputting to subtitle formats which preserve all caption information, particularly SCC and CCD, though those are somewhat niche formats. SubStation Alpha, while not a perfect 1:1 match, would preserve positioning information better than SRT and is more widely supported than SCC or CCD. Having SSA/ASS as the default conversion format with an option for 1:1 capturing with SCC would at least be an improvement.
EDIT: Unfortunately, CCExtractor does not preserve positioning information when converting to SubStation Alpha or any other more conventional subtitle format. Positioning info is only preserved in SCC, CCD, and the CCExtractor-specific formats like RAW and BIN.
I normally wouldn't post a message to bump my own topic, but I made this post just as chaos was erupting over the issue with keys being unavailable. Now that the situation has been resolved I'm hoping this suggestion might get some attention.