I've requested this before because I thought it made sense at the time. However, I found out that there's actually a way to use MB to fix file-naming errors like this without resorting to having to relocate each individual files. As no one told me, I'll tell you now.
If you've got to change the name of a folder, then the best thing to do is to select all the tracks that are in that folder in your library. Then you right click, go to Send To>Folder (Move) and select either Folder or Organised Folder. What this does is move all the files and delete the old empty folder at the end.
If you've got to change the name of a file, then select the track and hit shift and enter. If the track title or number differs from the file name, you can click on Rename at the top of the tag editor, and MB will rename the file for you.
Both of these processes preserve the references to the files in your library correctly. Hope that is all comprehensible and helpful!
Bold words in my posts are links unless expressly stated otherwise. Have fun with them!