here is another flat file db that ive been eyeing:\nhttps://github.com/sergeyksv/tingodb
upward compatible with mongodb.
Ive also used nedb, which is ok but tends to delete the datastore when it runs out of disk space :P
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.
Could you post an issue on https://github.com/louischatriot/nedb with your environment details and how to reproduce this?