Best practice is to keep your inbox as tidy as possible, since it's most susceptible for corruption. Move message you dealt with to a different folder, or simply delete them. The most likely reason for problems with mail file corruption is anti-virus software. Therefore it's recommended to create an exception in your anti-virus software for the Thunderbird profile folder, so that the anti-virus real-time scanner will not scan it. https://support.mozilla.org/en-US/kb/profiles-where-thunderbird-stores-user-data#w_how-to-find-your-profile It is quite possible that anti-virus software is involved in the effect you're seeing (if not causing it in the first place).