If you use the exact same file name, MC will keep everything the same. I've done this quite a few times with both audio and video files. My general approach, which I stole from someone else's forum posting about this same thing, goes basically like this:
1. Use the RM&C tool to rename the file to a very simple name. For audio files, I use the track number. So: 1.flac, 2.flac, etc. For video files, I usually use one or two characters of the title. So Heat.mkv becomes h.mkv , for example.
2. I take the new file and rename it exactly the same, like h.mkv . Then copy it over the top of the existing file, which wipes out the existing file, replacing it with the new one.
3. In MC, I then run Library Tools > Update library (from tags). This grabs all of the new format information like CODECs, run time, etc.
4. For consistency, I then rename the file back to my normal naming convention. For movies, this is the movie title. For audio, I have my own thing and I'm sure you do too.
In some cases, I like to keep both the DVD version and the BD version of a movie. Why? In some cases there is more or different footage in one version of the movie compared to the other. In these cases, I'll just make a new file name and let MC import it. Then, after MC imports it, and grabs the cover art and information, I edit it's name to reflect which version it is. So Armageddon becomes Armageddon (BD) or Armageddon (1080). That way I can distinguish one version from another.
Brian.