I wonder if it's possible that it was a MongoDB glitch and not a user error. From what I've read, it's notorious for randomly losing records. Maybe the loop save triggered it?
I definitely don't attribute this to MongoDB (or MongoEngine or pymongo or Django). I haven't seen it lose any of our documents to date. Silently dropping documents when saving them without making any changes would be a huge problem. It's astronomically unlikely.
It just seems hard to believe you confused 'save' and 'delete'...