By default @Query is considered to be a select query. To make it be treated as a modifying query, use @Modifying annotation:

Indicates a method should be regarded as modifying query.

So, you should write your repository the following way:

public interface PartRepo extends PagingAndSortingRepository<Part,Long> {
    @Modifying
    @Query(value = "SET IDENTITY_INSERT PART ON", nativeQuery = true)
    public void enableInsertIdentity();

    @Modifying
    @Query(value = "SET IDENTITY_INSERT PART OFF", nativeQuery = true)
    public void disableInsertIdentity();
}