I've done quite a few of these types of operations. I got my start with this from this wiki article, which outlines the process:
https://wiki.jriver.com/index.php/Re-Rip_and_preserve_tagsMy version goes something like this:
1. Rip files to location not monitored by MC.
2. Set the ripping application to rip using a very simple name. For audio files, I just use the track number. So 1.flac, 2.flac , etc.
3. Find the album in your library and highlight all files. Then use Rename, Move, and Copy files to change the existing files to use this same naming scheme. So 1.mp3, 2.mp3, etc.
4. Copy the new files over top of the existing files. If the formats are different, then the files won't be replaced, but it's the same idea.
5. If you replaced the files (same file type), then MC now "has" the new files. If not, then you need to update MC to see the new file extensions. Use RM&C in UPDATE mode. Use the Find & Replace template to change the file extension. For example, if going from mp3 to flac, then do Find:mp3 ; Replace:flac .
6. Now MC should be pointing at the new files, but it needs to be updated to see the properties of the new files. Library > Update Library (from tags)
7. At this point everything should be consistent and MC should have the new files with the new properties (like bit rate, file type, etc), but it should also have all of the original metadata (play count, etc). The last thing to do is to change the file names back to your normal convention. So, use RM&C once more in Rename mode to name the back to whatever format you like. I use Track#_TrackName . I have this saved as a preset because I use it so often.
You may also want to remove the original files at this point. I always do.
Brian.