Database
[{bookings:[{allEventDates:[{dayBookingRef:"000127-D6"},{dayBookingRef:"000127-D5"}]}]},{"key":2}]
Query
db.collection.update({"_id":ObjectId("5a934e000102030405000000")},{$pull:{bookings:{allEventDates:{$elemMatch:{"dayBookingRef":{$eq:"000127-D6"}}}}}})