Make sure you have sidecar files next to your movie files and check your cover art location. If you have specified a folder for cover art and the movie covers aren't there you can right click the movie, choose cover art and save art to external location.
Then when you replace the old movie with the new file with the same name etc, it should work. If not, art is not lost and can be found with a right click, cover art, quick find option.
The sidecar files take care of all the tags so you should be good.