Checking thousands of EML files one by one is rarely worth the time. After multiple exports or merged backups, many emails look identical even though they are scattered across different folders. That makes manual comparison slow and increases the chance of deleting the wrong copy.
If you have a large collection, you might want to try
GainTools EML Duplicate Remover, an offline Windows utility designed to process EML/EMLX files without requiring an email client. It can search the whole archive or only selected folders for duplicate emails, making it much easier to do a bulk cleanup than to review each message.
Once you clean the duplicate heavy folders, managing, searching and importing the remaining EML archive becomes much easier.