Data loss through the compact process has become the number one support request, so something is wrong.
The release of Thunderbird 16 should have fixed most of these issues. Please post a support request on the get satisfaction support site if your still experiencing these sorts of issues,
Please be sure to try right clicking the folder selecting properties and then repairing it. (not this only repair the index, If real data loss has occurred it can do nothing) Lots of information about how and what is always good. Steps to reproduce a problem get it fixed far faster that those issues where magic is involved.
Unfortunately no one knows what it is that is wrong, or really when it 'became' a problem. I have posted in the past about compacting and stated that data loss does not occur at the time of compacting, at the moment I feel that is not the case. I may also have been in error then as well.
I am making no claims that I can fix your problem, or that your data can be restored, on the contrary, recent cases of data loss do appear to be permanent. The usual options of changing the entry on the View menu for folder to ALL does not work and neither does right clicking the folder, selecting properties and then the repair button. I do however encourage everyone to try them. At this point my desire is to try and establish some sort of base line that can be used to determine the cause.
Is there a fundamental bug in the compact process? If there is, it is well hidden. Millions of people have no problem, but an unfortunate few not only see this problem, but in some cases see it repeatedly. This leads me to believe, rightly or wrongly that there is a secondary issue required or more than one that makes the circle complete and result in the problem. Thus we need to start looking for similarities between users who have the problem, and we get to the whole point of this post, to ask people to provide information.
I have no idea if this will be useful, but your co operation is appreciated.