To have Thunderbird preserve your folder structure when archiving emails, e.g. if you have filters set up to move messages into separate inbox folders, then you’ll need to make a manual change to the Thunderbird config.
Edit -> Preferences (or Options) -> Advanced (section) -> Config editor (button).
# Click the “I’ll be careful, I promise!” button. # Search for ‘structure’. # Double-click mail.identity.default.archive_keep_folder_structure so that it toggles to true.
Now, when you archive a message, its folder structure will also be archived.
Reference: Tip: Preserve folder structure in Thunderbird archives
