When Windows Live Mail displays identical messages more than once, the duplicates are usually the result of repeated imports, restored backups or multiple mailbox exports. You can delete them manually for a few messages, but it gets hard when you get hundreds of email with similar subjects and attachments.
A more practical approach is to clean the exported EML files before reorganizing the mailbox. I would suggest GainTools EML Duplicate Remover, as this trusted offline tool works with Windows Live Mail EML files without requiring the email client to be installed. It compares the actual email details instead of relying only on filenames and helps remove duplicate messages while preserving genuine emails and attachments.
I hope this points you in the right direction.