Very rarely it's necessary to reset Settings or the Setup. When you start Mail Archiver with the Shift and Control keys pressed then you will see the following dialog:

Start Mail Archiver with reset dialog

The Settings (formerly Preferences) are in user/username/Library/Preferences/com.mothsoftware.mailarchiverx.plist . 

Mail Archiver Preferences

Deleting the file needs a restart of the computer because the values are cached. When you click on the Settings button all values are deleted instead. These days the Settings contain the window positions, fonts, recent items and the appearance information.

The bulk of the information for archiving is in the database plandata.db. The database is made empty when you click on the Setup button of the dialog. The database is in the Application Support folder:

Settings database PlanData.db