1. The setting in Thunderbird to allow antivirus to quarantine messages has nothing to do with this. It writes all new mail to the temp folder so antivirus product that do not scan email can have at it. Nothing more. So having it off is actually standard as there are few except defender that do not scan email. But that is also a large part of why I use defender. No pesky email scanner.

Personally I am guessing bit defender has quarantined or deleted you mail store. They work through Identifying a "threat" and asking you to authorized an automatic fix. Often this is the deletion of 20 years worth of email stored in that mail folder. This is why I exclude antivirus products from scanning my profile folder. There is no such thing a a "threat" in a stored email. Thunderbird does not execute scripts in the email and attachments are stored a mime encoded plain text so email in storage is not a threat. Even attachments pose on threat until they are decrypted and turned back into a file, and that occurs in the system temp folder where the antivirus already has access to kill the file. So I suggest you establish of bitdefender has deleted something imporant and how the bitdefender folks propose to recover your data if it has.