We match songs on the iPod with songs in MC by comparing the following tags:
[Name], [Artist], [Album], [Genre], [trackNumber], [Media Type]
So if any of these tags change, MC will view the files as different, and won't simply update the tags on the iPod*, but instead it will copy the file as a new file. If you have "Delete files not in Sync" turned on it should delete the old file. (Note: You will not see the "Delete files not in Sync" option if you are manually transferring files rather than actually "syncing" the iPod. In this case you will have to manually delete the "duplicate" files.)
If you change any other tags and have the option Tools > Options > General > Importing & Tagging > 'Update tags when file info changes' turned on and the handheld option to 'Resync if Date Modified has changed' is turned on the file should be resynced as the same file - updating the iPod database with the new tag changes.
*MC never really just updates the tags on the iPod, it retransfers the file, updates the iPod database with the new tags and deletes the old file.