I’ve lost several missions to this bug and I didn’t realize until now it was due to a bug. I always thought I somehow wasn’t careful.
When you load a mission (Load WP File), and then alter the mission and hit ctrl+s to open the Save As dialog box, the default file name is the loaded mission. If then you decide to cancel saving the altered mission (and thus have not altered the filename) by hitting “ESC”, the mission is saved, destroying the original copy of the mission.