<blockquote> If I compact local folders does thunderbird just clean up the mbox files thus removes deleted messages and thus it not change the mbox structure </blockquote> Exactly right. Having said that, for some reason many people think it would be a good idea to let anti-virus software scan email. It isn't. Anti-virus software is the no. 1 cause for mail file corruption. In that case compacting can only try to repair the damage done previously by anti-virus software. To the uninformed user this then looks like Thunderbird lost messages. Creating regular backups of the Thunderbird profile is therefore highly recommended. https://support.mozilla.org/kb/profiles-where-thunderbird-stores-user-data#w_backing-up-a-profile