Haven't you a 'Save As' facility that allows you to save the email under a different filename. Or, you could save an email to second temporary folder, then 'Rename' the file, and transfer it to your original email folder.
I have managed to do it although I had to transfer them singularly .
I made a temporary folder and when I came across one with the same name i transferred it inti the temporary folder altered its name and then put it back into the copy folder as you said.