I think this would be a useful feature but find Redwing's suggested implementation overly complicated.
For one, it assumes everyone uses the Inbox which isn't true.
For two, it means moving your replacement file to a monitored folder to make it appear in the Inbox, which seems unnecessary because you're only going to move it again anyway.
For three, if you haven't tagged your replacement file (and there's no point, because you're about to replace all of its tags anyway), you won't easily be able to identify which track will be the replacement unless you display all the file paths which would be messy.
I think it would suffice if the "Replace file" menu command just displays a standard file browser dialog to select the replacement file. MusicBee can then take care of the file moving, renaming and tagging.
Bee excellent to each other...