You can fix this without sorting every email manually. When you merge EML folders from different computers, you often encounter duplicate messages because the same emails are present in multiple backups. An EML duplicate remover will be able to compare email properties, not just file names. This helps get rid of repeated messages while retaining original emails.
I had a similar issue when I was trying to organize an old email archive and realized that manually checking through thousands of files wasn’t an option. Using a tool like TrustVare EML Duplicate Remover made the process much easier as it can scan multiple EML folders, detect duplicate emails across or within folders, and save a cleaned copy separately. That also gave me a chance to verify the results before replacing the original archive.
Whichever method is used, keep a backup first. It makes it easy to restore the archive if anything unexpected is found after the cleanup.
