This would have reduced the file size of the mbox file and auto created a new index file and is a necessary part of good maintenance. If you compacted the folder, then 'marked as deleted' emails would have been fully removed. It would not have altered the size of the mbox file. msf file or 'Repaired Folder' method does not remove emails as there are no emails stored in the index files. msf file manually via profile folders whilst Thunderbird was closed or right clicked on folder, selected 'Properties' and then clicked on 'Repaired Folder', the selected *.msf file was deleted and thunderbird created a new one, scanned the relevant mbox file and the index is now showing you what actually exists in the mbox file. So you can end up with an index file out of synch with it's mbox file. But they do not scan or do anything with the. They are not always very good at understanding one mbox file may contain several emails. It may have scanned an mbox file and attempted repair, unfortunately Anti-Virus products are not always very good at this and they can corrupt a file or even cause a total loss of file. The most common reason for this is an Anti-Virus product. Maybe there were emails listed in the Thread pane which when selected showed as empty. msf index file did not match what was actually in the mbox file, so it was showing incorrect data. For some reason the index file used to display the list of emails in the 'Thread Pane' was out of synch with the actual storage of emails stored in the mbox file.
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