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. The .msf index file did not match what was actually in the mbox file, so it was showing incorrect data. Maybe there were emails listed in the Thread pane which when selected showed as empty.

The most common reason for this is an Anti-Virus product. 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. They are not always very good at understanding one mbox file may contain several emails. But they do not scan or do anything with the .msf file. So you can end up with an index file out of synch with it's mbox file.

When you deleted the .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.

The action of deleting the .msf file or 'Repaired Folder' method does not remove emails as there are no emails stored in the index files. It would not have altered the size of the mbox file.

If you compacted the folder, then 'marked as deleted' emails would have been fully removed. 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. But if folder was corrupted by AV product or a lack of compacting or any other reason etc, then compacting made it impossible to recover anything in the mbox file. So, if you have not compacted the folder then please do not compact anything at this point in time.

Are you talking about a POP or IMAP mail account? Do you have any backup of profile?

Thank you. I'm not exactly sure how it was fixed, but your bit on the virus scanner and then I paid more attention to another post about checking the virus chest (There was an unsuffixed inbox in there) may have been the solution. I restored the virus chest inbox and I was trying other stuff and shazam! my emails were back. So, thank you.