"Remuxing" is the process of taking the original video and audio and putting them into a new, cleaner container without losing quality.
Keep the highest-quality track (like DTS-HD MA or TrueHD) and perhaps one standard AC3 track for compatibility with older devices.
Look for the largest video track. If your source has multiple large tracks (common with "extended" or "theatrical" editions), you may need to check the segment map or duration to find the correct one.