[sn]

I still remember this problem. To my best knowledge nobody else has ever had data loss after a clean shutdown and no hardware problems.

It sounded to me like it could have been the same problem as this person encountered: https://stackoverflow.com/questions/10560834/to-what-extent-... . Based on their data loss after a clean shutdown of mongodb in order to perform a backup, I think the only way we could have possibly saved the data is if we hibernated the system instead of doing a clean shutdown. But I don't know how well mongodb handles sudden time jumps. In general, since time jumps can be an issue, we typically perform shutdowns if a service needs to be stopped for whatever reason.

I hope you ended up with a hosted mongodb service or an MSP with an expertise specifically with mongodb, as mongo seems like it can be very tricky to administer properly if it's not the one thing you do.