[quote user="breezes"] 1) Why are the moved emails not deleted from the "copies to self" folder?   [/quote]

I don't have an explanation as to why you aren't seeing them deleted.  I would restart Pegasus Mail then test using both the Move button and drag and drop.  Both methods should work.

[quote user="breezes"] 2)  Why is Pegasus willing to make two copies of the email in John Doe's folder, same datestamp and content, rather tan saying "Look here dummy, you already have that email in this folder"?[/quote]

Messages stored in folders are not stored as individual files but appended to a single file.  Pegasus Mail does not check the content of the folder file for duplicate content when you add a message to it. 

I've been re-organizing my mail folders and have run up against something I don't understand, and find troublesome.  I have decided to integrate outgoing mail with incoming mail for specific correspondents.  I want to be able to open a mail folder, for John Doe, and and read his mail and my responses, in proper sequence, without moving back and forth from his folder to saved copies to self.  In doing this I have moved my responses from "copies to self" into John Doe's folder, where they are sorted by date along with his incoming emails.  It's good sequential integration, makes things easy to follow.  I have moved approximately 1000 emails, copies to self, into John Doe's mail folder.

Then comes the confusing part.  I moved all that mail, see that it's added to John Doe's folder, but it is not deleted from the "copies to self" folder.   I move them all again from "copies to self" to John Doe's folder.  They move successfully but are still not deleted from the "copies to self" folder.  However, I now have two copies of the moved mail in John Doe's folder.

 Two questions:  1) Why are the moved emails not deleted from the "copies to self" folder?   

                        2)  Why is Pegasus willing to make two copies of the email in John Doe's folder, same datestamp and content, rather tan saying "Look here dummy, you already have that email in this folder"?