What does Mark as Done do?
Mark as Done moves the mail to the “Done” tab and marks it like that. It means there is nothing more to do with this mail, but it is still valuable for you to keep.
Using More | Global Settings | Auto Mark as Done setting, you can cause replied messages to be automatically marked as Done. By default this setting is Off.
Note: That if you use the Incoming Filter you won’t see emails marked as done.