I get a message that says I'm about to override Thunderbird, which freezes Thunderbird and asks me to confirm security exception.
It's a long error message that says "You are about to override how Thunderbird identifies this site" and goes on to to say the certificate for my server is outdated and I should confirm a security exception. It also freezes Thunderbird so no commands are accepted.
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It is supposed to freeze, until you allow the exception or disallow it. An even better result would be for the certificate in question to be updated so no exception is required
Contact the mail server operator (your mail provider) and ask them what is wrong with their certificates.