You could try to manually setup the PrefetchPathElement object, with a manual entityrelation object, like done in the generated code.
Here is the constructor of the PrefetchPathElement
public PrefetchPathElement(
IEntityCollection retrievalCollection,
IEntityRelation relation,
int destinationEntityType,
int toFetchEntityType,
int maxAmountOfItemsToReturn,
ISortExpression sorter,
IPredicateExpression filter,
IRelationCollection filterRelations,
string propertyName,
RelationType typeOfRelation
);
Though it's not said it will work, as values for PK and FK have to be EQUAL to make a match between parent and child.