Ok, I m not the guru of compacting, but I will share my knowledge/experience and you've been waiting awhile. Compacting removes deleted messages from the folder, and it also rebuilds the index. A possible cause of confusion:: When a search is done. the global search uses the index, and users may rely on an older search after a message has been deleted. That is,, a search may indicate a message is present when it is not. There are millions of Thunderbird users; if messages were being deleted, even for 1% of users, there would be a massive outcry.

Regardless of our confidence in Thunderbird, as a business, I recommend daily backups because you are more likely to encounter a computer failure or a software crash or a virus infection. Having written that, many backups don't work, as evidenced from what we see here on the forum. The simplest backup that always works is this:

1. If IMAP, do File>offline>download (to ensure all messages are on PC)
2. ensure thunderbird is not running <== IMPORTANT
3. enter %appdata% in search window on task bar and press Enter key
4. this should open windows file explorer in Appdata\roaming folder
5. highlight the Thunderbird folder and copy to external media

Those are the basic mechanics, but a detailed assessment of potentially lost messages since last backup is encouraged. For your question no how to restore 'lost' messages, I do not feel that is possible, as the messages may likely have previously been deleted. Othes may see possibilities.

1. Please always state your version.

2. You wrote "Your information indicates that compacting would not cause any data loss." - where are you seeing this documented?

3. It is true that compact should not cause dataloss. And compact was rewritten in the past year, and tuned, to make this much better. But it can happen. It would be helpful to know what happened on your computer in the day(s) leading up to this failure - power loss? virus? rebooted without shutting down Thunderbird? anything else unusual? (more info at https://support.mozilla.org/en-US/kb/compacting-folders-potential-complications )

4. As for recovering from your present situation, in addition to what david has stated, "compacting would not cause any data loss ... has not been the case." is unfortunately vague. Please elaborate on exactly, precisely what you are seeing (or not seeing).

More background at https://support.mozilla.org/en-US/kb/compacting-folders

Regarding item #4, I now see you have stated "nearly all my my e-mails that were stored in subfolders have disappeared." in https://support.mozilla.org/en-US/questions/1513163/

Is it just one or two folders that are affected, out of your many folders? Are they first level folders under your account? Or are they all second level or lower subfolders? What is your AV software?

This problem should be gone in current versions, with compact enabled.