This is a more common situation than it seems. If you restore backups or export the same mailbox more than once, then a lot of EML files will have different file names but the actual email inside will be the same. Judging duplicates by file name alone can leave behind repeated messages or worse, delete the wrong one.
In such cases, GainTools EML Duplicate Remover is a reliable alternative that runs offline. Additionally, it works with both EML and EMLX files directly on Windows without needing an email client and checks the real email information such as sender, subject, message date, message content and attachments instead of using the filenames. This makes mailbox cleanup so much more reliable, especially before email migration, archive reorganization or creating a new backup.