You can modify the passed object in the "call a microflow" by setting the assocation.
My approach to achieve this was:
1) Create import via mapping of parent (using a key if you like). Use the list in your flow (e.g. ParentList). (Not included in the picture!)
2) Create import via mapping of the children: create new objects (do NOT find by key). Use the list in your flow (e.g. ChildList).
3) Iterate over ParentList. Within this iteration, iterate over ChildList. Within this double iterator, do a 'RetrieveOrCreate' based on your Parent and any key of your child you like.
4) After the RetrieveOrCreate, change the retrieved/created child by setting the values from the iteratorChild.
5) Commit the RetrievedOrCreated items. They the children that are unique to a parent and perhaps a key you have defined in your RetrieveOrCreate flow.
6) Delete the ChildList from Step 2). This makes sure only children are created which refer to a parent.
Hope this helps!