The error and the visual disappearance of your mail were probably directly related. Do you have an exclusion in your antivirus program for the Thunderbird profile folder?

That is the most common issue with compacting. Antivirus programs lock files and you get messages about disk space because the program can not make the file bigger because it is locked by the antivirus. An exclusion to keep the interfering program away while Thunderbird is running is the simply cure.

I added an exclusion to my Norton for the whole Profiles directory. Many days later and after shutting down and starting up my laptop many times, Thunderbird asked to compact my Inbox and the same error occurred again. So this appears to be something other than AV software interference.

I'm also sometimes seeing the blank Inbox after compacting was triggered automatically. But it isn't exactly reproducible. And I have no idea what triggers this behavior. A Thunderbird restart is needed to clear this up. I'm also seeing this on Linux, so I do agree, the blank Inbox effect has got nothing to do with anti-virus software. Unfortunately without exact steps to reproduce there is no point raising a bug. I do not see any error messages in connection with compacting.

This time I got an error (sorry I did not save the exact error message) but it was that the folder could not be compacted due to an error, possibly not enough disk space and to check and make more space available.

This kind of error may very well be caused by anti-virus software.