Sounds like the repair did work. As it simply rebuilds the index into the existing database of mail, that it now shows nothing would indicate that either the store is corrupt, or more likely empty. In the case of POP mail accounts I have seen antivirus product "quarantine" every mail in the last however long you have used Thunderbird as they are all stored in a single file. All because it has detected something that will never hurt you or your computer. I have even seen that set to delete mail containing threats which has deleted everything in a years old inbox file. Is your account IMAP or POP? Are you starting with newly received mail in the folder as they arrive?