Emails are stored in mbox text files eg: Inbox Thunderbird uses another file called 'Inbox.msf' as an indexing file, so this is used to display the list of emails, then when you select and email, it knows where to look in the Inbox mbox for the actual email which is then displayed.

If the Inbox.msf file has become out of synch showing issues like you mention, often a 'Repair Folder' will force the Inbox.msf file to be removed and new one created where it reads the mbox file and is updated. It does not delete emails and it does not effect the actual mbox file storing the emails.

If the Inbox mbox file that hold emails is empty then the newly created Inbox.msf file cannot show what is not there.

So, why is the Inbox mbox file empty ?

If the mbox file became corrupted and was then compacted to remove all hidden marked as deleted emails, (which occur when you either move or delete emails) then it may not be able to read which emails were marked as deleted and so ends up empty. Corruption can occur if compacting has not been done on a regular basis or not been performed at all.

Perhaps the most common cause of Corruption occures if an Anti-Virus product has scanned the file and tried to fix it or quarrantined the file. Anti-Virus products cannot work out that the mbox file contains many emails, it just sees it as a single file - which it is and nobbles the entire file in one go. Anti-Virus products usually have no effect on the Inbox.msf file as it does not contain emails, so it is left alone, hence why you appear to have a list of emails. The result being the index (msf) file is trying to find something that has already gone, so weridness abounds. After a fix of index file, it shows what is really in mbox file.

My advice: Compact the Inbox on a regular basis. I would also compact the Drafts and Junk as well as they will get a load of deletions.

Do not allow Anti-virus products to scan any Thunderbird profile folders, so make them exempt from scanning. If you do want to scan them, I suggest you alter settings so the Anti-Virus asks what to do, then you can stop any 'fix' by the AV. Under no circumstances do you want any AV or other product that cleans up files anywhere near your Thunderbird profile folders.

Thank you, Toad-Hall, for taking the time and trouble to explain what is a bit of a minefield ! Firstly, I try to keep my mailboxes in some sort of order. I religiously compact whenever prompted, and regularly empty the Junk and Deleted folders. I try to minimise the size of the Inbox by archiving every month or so. In fact, it was during one of these 'tidying-up' sessions that the problem arose. Working through a couple of hundred messages and moving them to archive, it became apparent that a few of them were misbehaving, refusing to open, etc. Obviously a corruption somewhere, and the general advice was to do a Folder Repair, not expecting disastrous results. I am going to suggest to Mozilla that they re-name this function Folder Delete. I have used anti-virus (Kaspersky and now Bitdefender) and Thunderbird for many years without problems. So I have to keep fingers crossed... thanks anyway.

re :I am going to suggest to Mozilla that they re-name this function Folder Delete.

But 'Repair Folder does not delete the Folder nor does it delete emails. It refreshes/repairs an index file which gets it's header data from the file that stores the emails. It does not do anything with the file that stores the emails nor does the index file contain any emails itself. By the time you realised there was a problem, prior to performing the 'Repair Folder' the file (mbox) that contained the emails, was already being corrupted.

re: Obviously a corruption somewhere, and the general advice was to do a Folder Repair, not expecting disastrous results. I agree.

Bitdefender would be the most likely cause of your problem. Anti-Virus products have been a continual issue when it comes to files that store emails. Bitdefender may be able to scan all files on boot up of computer. It may have real time protection operating and so is scanning incoming mail and any files get get opened. When you selected the Inbox and started to move emails to another folder, you are opening that file, it is likely Bitdefender was also scanning those opened files. So, whilst you and Thunderbird were attempting to perform an archive, Bitdefender was also opening and scanning those files which were in the processes of being updated. Bitdefender has no ability to realise that one file has lots of emails. https://www.bitdefender.com/consumer/support/answer/13450/

I strongly suggest you stop Bitdefender from having the ability to scan your 'Thunderbird' profile folder (and any folder or file contained therein) which by default is in this location: C:\Users\<Windows user name>\AppData\Roaming\Thunderbird\