When you make external changes to files that MC has imported, you are effectively pulling the table cloth out from under the dishes. This is not a normal mode of operation for MC. This isn't a big deal or anything.
As I understand it, the proper way to tell MC to update a file is to use Tools > Library Tools > Update Library (from tags) . However, be aware that this re-reads the metadata tags inside the file: Album, Artist, Name, etc. So, if you have made edits to those fields and they are NOT saved inside the file, your MC values will be overwritten with the values that are in the files.
I use the MC option that writes all tags back to the files as soon as they are changed. MC is my "library master" so I want the files in sync with MC's values.
All that said, I would have expected that doing Analyze Audio on an edited file would update its duration as well as the various audio dynamics fields. I'm fairly sure that Update Library (from tags) updates EVERYTHING. I have occasionally had to do this when I pulled the table cloth out from under my Library.
Best of luck to you,
Brian.