I have several labels. That gives Apple Mail a big reason to maintain a large number of folders. I am looking out for a solution that can backup my Mac Mail folders.
I have been working with a paid software named Mail Backup X. Though not in hundreds, I too have quite many mail folders. Amazingly Mail Backup X backs up mac mail folders and all their emails perfectly. The tool has an option to auto update the folders. That is if you add new folders to your account, that will be instantly reflected in your Mail Backup X Viewer, and thus to your back up locations. For reference, you may read this article:http://www.mailbackupx.com/how-to-scenerios/how-to-backup-apple-mac-mail-mails-on-mac.html