Transfer Tool Overwrite doesn't remove deleted files

When you transfer an account to a server, and then later you transfer the same account to the server and use the "overwrite" option, it does not delete files from the destination that have been removed from the source. So, for example, the source contains file1.txt and you do a transfer, that file transfers, good. Now, that transfer is not live yet, you are just doing an initial transfer so that the final transfer is faster (because it uses rsync to speed it up). The user deletes file1.txt. Then, you do another transfer with the overwrite option. file1.txt is still on the new server, and does not get deleted. Now, when the new server is live, the user magically sees old files. This is especially bad for emails, as the user now sees all the old emails that they recently deleted.