Duplicate EML files with attachments are tricky because two emails may look the same, but the attachment copy can still matter. I would not delete them manually unless you have checked the message headers and attachment details first.
A safer approach is to work on a backup folder and use GainTools EML Duplicate Remover as a practical offline option. It can check EML/EMLX duplicates without needing Thunderbird, Windows Live Mail or any other email client and it keeps attachments, email properties and folder order safe during cleanup. The option to remove duplicates within one folder or across all folders is useful when the same message exists in several exported mail folders.
Run the demo on a few sample EML files first. Once the attachment copies look correct in the result, you can clean the full archive with greater confidence.
