I just had to fix a problem in Thunderbird causing messages to reappear after having deleted them. Annoyingly, some messages also showed up as blank (see screenshot above).
For a possible solution to this problem, follow these steps:
1. Right-click the Inbox folder.
2. Choose Properties from the menu that opens.
3. Click on Repair Folder.
Why I am using Thunderbird
As a user, I found myself wondering if Thunderbird was bugged or had suddenly become unreliable, like Microsoft's Outlook Express and Windows Live Mail in Windows. The reason I started using Thunderbird was to replace Windows Live Mail since Microsoft decided to end support for their free e-mail client again. It happened with Outlook Express, and it was happening again with Windows Live Mail.
The build-in mail app in Windows 10 is very limited, and does not come anywhere near a useful replacement to Windows Live Mail.
It is really important that the software we use everyday is software we can trust to not suddenly stop working. The good thing about Thunderbird is that it is open source, hence if something stops working, it will likely be fixed by the community.
What causes reappearing and blank messages
In my opinion, this is a bug in Thunderbird, and logically it should be easy to fix.
Apparently, this is caused by corrupted inbox files. One or more "bugs" in Thunderbird is causing this problem, but luckily the developers created a dirty "hack" that usually fixes it.
Simply right-click the Inbox folder and choose Properties from the menu that opens, then click on Repair Folder.
I do not know exactly why it happens, but maybe it has to do with the way Thunderbird is storing e-mails locally.
Seperate files vs one big file
In my opinion, storing messages as separate files would be better for users. It is what users intuitively will expect to happen behind the scenes. Storing messages in a single text-file is potentially dangerous, and if developers are not extremely careful, such files could break, potentially causing the user to loose important e-mails.
Another benefit of having a separate file for each e-mail is that the user can easily move them around, as well as open them in whatever text-editor or app they want. Instead, Thunderbird is storing all e-mails in a single file.
The above is not only inconvenient for users who wish to move their e-mail around easily, it likely also complicates it for the developers of Thunderbird, since now they have to edit this file very carefully when messages are deleted. Apparently, this is also what causes the strange design/behavior of prompting users to "compact messages".
I have always wondered why some e-mail clients would prompt me to compact my e-mail messages. For a long time, I thought it had to do with compression. For this reason, I would nearly always dismiss it when prompted, worrying it might cause me to loose e-mails.
Compacting is the process of deleting messages that has been marked for deletion, and has nothing to do with compression. However, if Thunderbird instead stored messages in individual files, the need to "compact messages" would not be there.
Backing up e-mail via your file manager
This is something I have personally done many times, but as far as I remember, the exact way you had to go about it would change every time Microsoft updated Windows, or decided to end support on their e-mail client. The lack of support and reliability was what caused me to move to Thunderbird.
Microsoft has also made it notoriously difficult for users of their e-mail programs to locate the folder where e-mail is stored. Knowing the location of e-mails, on your file system, is important if you want to import or backup e-mails within the drag & drop convenience of the file manager. It could be done for MS e-mail clients – but it was not easy.
With Thunderbird, this is somewhat easier. But, I would still prefer a standard location of e-mails. In Linux, e-mails could be placed in a convenient place like /home/YourUser/mail, but instead it is located in a long and obscure path like the below: