A trackback got through on MT, and ended up causing a rebuild that overwrote the stylesheet, index.php (which is the WP template), and various other files. Luckily, this time I had backups.
Trackbacks should have been turned off, but with all the hacks to overcome spamming, turning TB off in the database isn’t reliable.
If you do move from MT to WP, you’ll have to move the MT installation. Completely. You can’t trust that something won’t sneak through and cause a rebuild.