Many to many update in MongoDB without transactions

Question

I have two collections with a many-to-many relationship. I want to store an array of linked ObjectIds in both documents so that I can take Document A and retrieve all linked Doc

Answer 1

Should I use safe mode and manually check the data went in afterwards and try again on failure?

Yes this an approach, but there is an another - you can implement an optimistic transaction. It has some overhead and limitations but it guarantees data consistency. I wrote an example and some explanation on a GitHub page.