Mail deleted a large number of messages but not all of them. It was stored in files (which were smaller on disk, so not an indexing issue) and recovery required loading snapshots from Time Machine, converting to a format Thunderbird could import and transitioning to that.
You've only addressed something like 30% of the issues I asked about (although I'm honestly impressed you got that far), e.g., I wouldn't call Apple Mail an application designed to managed a collection of emails on disk. Isn't the important question here whether the emails were still stored on the server? E.g., or were they using POP?
