Compacting does not delete emails. https://support.mozilla.org/en-US/kb/compacting-folders It looks at the mbox file containing emails and then copies all emails that are not 'marked as deleted' to a file - eg: all good emails and then saves the file. If the file was already corrupted then a problem can occur. But even so it should not effect all of your folders. ''I agreed to compact files on Tuesday evening'' Then you should have seen all the folders etc on Tuesday evening after compacting. If you exited Thunderbird too soon whilst compacting was occuring then corruption may occur on opened files. But Thunderbird usually creates nstmp folders if interrupted. https://kb.mozillazine.org/Nstmp_folders Do you see any nstmp folders in the profile folders ? Do you have an Anti-Virus set up to scan opened files or perform backup etc because they can cause all sorts of issues? What OS do you use? What version of Thunderbird do you use ? Are you talking about an Imap or Pop account ? If Pop - do you keep a copy of messages on the server? Have you ever backed up your profile folders to an external disk drive/usb, so you have an independent copy of emails? Did you start Thunderbird and get asked to create a mail account ? If yes, then did Thunderbird perform an auto update ? * Settings> General * scroll down to updates section and click on 'Show update history' Does it say an update occured during the night? Do you have any updater software on your computer controlling updates? Some Anti-virus software also offer the ability to check programs for updates. This is important because you do not want any other software controlling updates - only Thunderbird should manage this. You would not want auto updates occuring if Thunderbird was still performing operations. Nor would you want Anti-Virus performing checks etc.