Yes, you can clean duplicate EML emails from a Thunderbird backup before importing it to another system. Doing this first helps avoid repeated messages, larger mailbox size, and confusion after migration.
The better route is to clean the exported EML folder outside Thunderbird instead of opening every message manually. A suitable choice here is TrustVare EML Duplicate Remover, as this privacy friendly Windows utility supports Thunderbird EML files, works without any mail client, and can check duplicates within folders or across the full backup.
It also helps retain attachments, email details, and folder order during cleanup. Before moving data to the new system, run the trial version on your Thunderbird backup and confirm the duplicate results.
