My main folder no longer shows up on the left folder panel.

I have no idea what your 'main folder' is. Can you provide more details? You may also want to provide a screenshot of your problem. http://support.mozilla.org/en-US/kb/how-do-i-create-screenshot-my-problem

The emails and their content are in the database when the Sqlite file is viewed from s 3rd party app.

Thunderbird does not store messages in sqlite format, it uses mbox.

The Thunderbird search app finds the emails, but when you open the email, there is no content.

What you see is probably the information from the search index.

Thanks for the reply. I was able to restore it by using an older backup (I'm gonna do it more often) and then copying the current Sqlite index and mail folder into the folder.

My "main" folder was my main email account that Thunderbird renamed "main" since I selected it. Basically, my most active email account entirely disappeared.

It's interesting that thunderbird does not store the emails in the sqlite database. Using a sqlite viewer, I could see the entire emails.

Thanks for your help.

Glad you were able to fix the problem. And you appear to be one of the few people who actually bother to create a backup, as opposed to many others. Can you then mark your response as 'Solution' for the thread please? Thank you.