Nitpick: I would probably have written this with a unique loop and a switch statement to decrease cyclomatic complexity and increase clarity.

        // Remove relations not present in input set
        foreach ( $mappedRelations as $relationType => $relationData )
        {
            foreach ( $relationData as $relationEntry )
            {
                switch ( $relationType )
                {
                    case Relation::FIELD:
                        foreach ( $relationEntry as $relation )
                        {
                            $this->persistenceHandler->contentHandler()->removeRelation(
                                $relation->id,
                                $relationType
                            );
                        }
                        break;
                    case Relation::LINK:
                    case Relation::EMBED:
                        $this->persistenceHandler->contentHandler()->removeRelation(
                            $relationEntry->id,
                            $relationType
                        );  
                }
            }
        }