search and facet api tables dropped during module updates
This issue is resolved, thanks to an insight rocketeerbkw provided about the drush up process. I changed my user umask setting to 022 in .bashrc to be more permissive for files that my account creates on the server. This completely resolved the database table dropping issue. Before I changed the umask, I had been running drush using my normal user account with a private umask setting, and when drush downloaded new files for updates, the resulting strict permissions broke any cache rebuilds that might have been involved and also on occasion broke the database connectivity. This was neither a MySQL nor drush issue.