NeDB creator here. I'd like to know more about the issue you're describing, I've never heard about it and considering the test coverage I just don't see how it could happen.
Sure, for some reason I thought this was a known issue. I saw it mentioned somewhere else on github - but its can't be that well known since you don't know about it. Ill open an issue this afternoon.
Could you post an issue on https://github.com/louischatriot/nedb with your environment details and how to reproduce this?