I just merged 6 mailboxes together, and I noticed some duplication.
I had one mailbox in a folder “Computer” called “grenouille”. I had 5 mailboxes called “grenouille”, “grenouille-1”, … “grenouille-4” in my Library. I selected all the folders and did a merge, and the 4 messages in the Library “grenouille” mailbox were duplicated.
I tried merging this mailbox and another that has 7 messages and both were moved to the trash and no new mailbox appeared.
Note that the mailbox in question is one that has the weird extra From lines that prevented it from displaying.