I can't explain how filters could come and go like that, as it's never happened to me. But you can make recovery easier by backing up the filter files. Actually, you should consider making regular backups of you entire Thunderbird Profile, but if you're just interested in the filters, they are in files called "msgFilterRules.dat", one file in each account folder. For example, in Windows, with an IMAP account, the filter rules file would be found in: C:\Users\<your logon name>\AppData\Roaming\Thunderbird\Profiles\<your Thunderbird profile>\ImapMail\<email account name>\msgFilterRules.dat Make a copy of those files to a safe location and restore them when necessary, while Thunderbird is closed. One thing occurs to me - could your antivirus be falsely flagging and quarantining them as virus/malware?