Folders in Mozilla Thunderbird can sometimes lose track of their underlying structure. As a result, archived messages may go missing, or previously deleted emails might suddenly reappear. Here's how to repair Thunderbird folders in case this happens to you.
Instructions in this article apply to Thunderbird version 68.6.0 for Windows, macOS, and Linux.
How to Repair Thunderbird Folders
To make Thunderbird rebuild the folder index and make it accurately reflect the messages you currently have in the folder:
Turn off automatic mail checking in Thunderbird as a precaution. This may not be necessary, but it can prevent potential conflicts.
Right-click the folder you want to repair and select Properties from the menu that appears.
Go to the General Information tab and select Repair Folder.
You don't have to wait for the rebuilding to finish before clicking OK; however, you should not do anything else in Thunderbird until the rebuilding process is complete.
How to Rebuild Multiple Folders in Thunderbird
To have Thunderbird repair the indexes of several folders automatically:
Make sure Mozilla Thunderbird is not running.
Open your Mozilla Thunderbird profile directory on your computer and select the desired account's data folder.
IMAP accounts are in the ImapMail folder; POP accounts are found under Mail/Local Folders.
Locate the .msf files that correspond to the folders you want to rebuild and move them to the trash.
Do not delete the corresponding files without the .msf extension. For example, if you see a file called Inbox and another file called Inbox.msf, keep the former and delete the latter.
Start Thunderbird. The email client will rebuild the removed .msf index files, thus repairing your folders.