With Eudora, close it down, browse the underlying file structure and rename the *.toc file to *.old. This is the Table Of Contents, and it's function is there to index the other associated mailbox file (which contains the emails themselves).
You will lose the read/unread nature of the email, but it should reduce/remove the duplication issues encountered.
(note: this support information is 15 years old, and as such they may have changed the product since I supported it, so the usual caveats apply).