Yes, you would select the messages in the EagleFiler smart folder and choose File ‣ Export, and then import the file into Mail as described at the link above.
when I import the files in Apple mail each mail is displayed in its own folder (that’s practically 200 folders with 200 mails)
but I want all the mails just put back in Apple Mail…without folders !
If the messages are stored in mailbox files in EagleFiler, when you choose Export it will make a new mailbox file containing the selected messages. If the messages are stored as individual .eml files in EagleFiler, Export will copy the files as-is. If you would like to combine them into a single mailbox prior to exporting, you could use the Merge Message Files command.