Bedankt jongens. Op basis van uw antwoorden kwam ik tot de volgende oplossing:
var mainDocumentId = "5807c22e959ca231f0c48a75";
var arrayItemId = "5807cc08959ca331f09c530e"; //Id for foo
var unit = new Unit(...)
var filter = Builders<UnitType>.Eq(o => o.Id, mainDocumentId); // optional
filter &= Builders<UnitType>.Filter.ElemMatch(o => o.Units, o => o.Id == arrayItemId);
var update = Builders<UnitType>.Update.Set(o => o.Units[-1], unit);
collection.UpdateOne(filter, update);