Thunderbird is creating TWO backup folders for offline use.
I was trying different ways and places to store backups of my e-mails as I use a shared computer. I first created a folder called "Thunderbird E-mail Backup" in My Documents and set this to be the offline folder. I then created a Locker-like folder that was going to require a password to unlock. It was a folder called "Locker" within My Documents that had a sub-folder again called "Thunderbird E-mail Backup". I changed the offline settings to save to this new folder and deleted the old folder, however, upon restarting Thunderbird, the original "Thunderbird E-mail Backup" in My Documents was re-created. I thought maybe it had to do with the password protected Locker folder so I created a new folder in My Documents called "Thunderbird Backup". I, again, deleted "Thunderbird E-mail Backup" and "Locker" with "Thunderbird E-mail Backup" sub-folder but upon opening Thunderbird it re-created the main "Thunderbird E-mail Backup" folder again. At this point Thunderbird continues to backup in two locations: "Thunderbird E-mail Backup" and "Thunderbird Backup".
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I've discovered that it is two different "backups". One is the local folder and one is the storage. I am still having one somewhat related issue: I have both items turned off and yet they still continue to store data. How can I ensure that these don't continue saving data on my computer.
I have no idea what you're trying to achieve.
Thunderbird stores all mail in the profile. Even though you can change the storage location, this isn't recommended, as most people have no clue what they are doing. So this will ultimately cause trouble.
In order to create a backup of your profile follow these instructions.
http://kb.mozillazine.org/Thunderbird_:_FAQs_:_Backing_Up_and_Restoring
I don't think it's possible to protect an individual mail folder with a password.
In general, you create folders from within Thunderbird, and not directly in the file system.