The Archive feature seems useless to me if you want to safely back up, archive, messages or mailboxes.
With Mavericks when I Archive a mailbox edits to either the source mailbox or to the Archive versions result in changes to the other.
It behaves as an alias of a folder or directory in the finder would, if you were editing the folder's contents.
So, I am doing this now and this might change, what I am doing is creating a workflow in automator to Export a mailbox, am giong to try a smart mailbox first, to a directory in Dropbox to be triggered when I receive an email from the snake whose emails I want a record of.
That way although they will over write, I think unless I can get them sequentially named, Dropbox will keep a copy of each through time.
So the Archive feature in Mail is not implemented properly or shoud be renamed to be Useless Alias of Mailbox