If you can relay on the assumption that the DTO's child collection is
probably the most updated version, you can actually replace the old
collection with the new one. We had the same issue with NHibernate and
we solved it like this:
1. Use ConstructWith to pull the entity out of the database using the
dto's id.
2. Use BeforeMap to CLEAR the entire child collection (make sure that
the reference on the child will be set to null as well).
3. AutoMapper will automatically copy the new collection.
Luckily, NHibernate was smart enough to apply changes only, I can't
tell if EF does the same.
This isn't a perfect solution, but it works for a simple domain model.