use the ImportExporttool.

• Install this addon tool: https://freeshell.de//~kaosmos/mboximport-en.html

Use the link and scroll down to bottom to see download.

   Save the xpi file to your desktop

• In Thunderbird, 'Tools' > 'Add-ons'
• Add-ons Manager opens in new tab
• click on the daisy wheel icon and select 'Install addon from file'
• locate the saved .xpi file and click on 'open'
• close and restart Thunderbird

Now use the tool to Export the folder or emails in the folder.

• Right click on folder > ImportExport tool >

select from options available such as:

   * you could 'export all messages in the folder' as 'eml' format 

See image.

The other option would be to copy the Local Folders folder from your Profile folders. These would not be saved as individual .eml files.

make hidden files and folders visible:

• http://kb.mozillazine.org/Show_hidden_files_and_folders

In Thunderbird

• Help > Troubleshooting Information
• click on 'Show Folder'
• Close Thunderbird Now
• click on 'Mail' folder
• copy the 'Local Folders' folder or click on that folder to open and copy the files with folder names (not .msf files).

I'd simply backup the entire profile.

http://kb.mozillazine.org/Thunderbird_:_FAQs_:_Backing_Up_and_Restoring