Hi.

Test project:

namespace ConsoleApplication1
{
    using ConsoleApplication11;

    using Xtensive.Orm;
    using Xtensive.Orm.Configuration;
    using Xtensive.Orm.Model;

    class Program
    {
        static void Main(string[] args)
        {
            var cfg = new DomainConfiguration("sqlserver", "Data Source=localhost; Initial Catalog=do40-tests; Integrated Security=True;")
            {
                UpgradeMode = DomainUpgradeMode.Recreate,
                ValidationMode = ValidationMode.OnDemand
            };

            cfg.Sessions.Add(new SessionConfiguration("Default")
            {
                BatchSize = 25,
                DefaultIsolationLevel = SessionConfiguration.DefaultDefaultIsolationLevel,
                CacheSize = 1000,
                Options = SessionOptions.Default | SessionOptions.AutoTransactionOpenMode | SessionOptions.AutoTransactionSuppressMode
            });

            cfg.Types.Register(typeof(Program).Assembly);

            var domain = Domain.Build(cfg);
        }
    }

    [HierarchyRoot]
    public class BaseEntity : Entity
    {
        [Field, Key]
        public int Id { get; private set; }
    }

    /// <summary>
    /// First entity
    /// </summary>
    [HierarchyRoot(InheritanceSchema = InheritanceSchema.SingleTable)]
    [Index("TestField", "TestLink", Unique = true, Name = "DescendantA.IX_TestFieldTestLink")]
    public class EntityA : Entity
    {
        [Field, Key]
        public int Id { get; private set; }

        /// <summary>
        /// TestField
        /// </summary>
        [Field]
        public string TestField { get; set; }

        /// <summary>
        /// TestLink
        /// </summary>
        [Field(Nullable = false)]
        public EntityB TestLink { get; set; }
    }

    /// <summary>
    /// Second entity
    /// </summary>
    [HierarchyRoot]
    public class EntityB : Entity
    {
        [Field, Key]
        public int Id { get; private set; }

        /// <summary>
        /// TestField
        /// </summary>
        [Field]
        public string TestField { get; set; }
    }

    /// <summary>
    /// Descendant
    /// </summary>
    [Index("Field", "TestField", Unique = true, Name = "DescendantA.IX_FieldTestField")]
    [Index("Field", Unique = true, Name = "DescendantA.IX_Field")]
    [Index("TestField", Unique = true, Name = "DescendantA.IX_TestField")]
    public class DescendantA : EntityA
    {
        [Field]
        public int Field { get; private set; }
    }
}

From three indexes on DescendantA in DB creates only second one. I think, it's logical with ClassTable scheme, but maybe should throw warning on update scheme step.

With ConcreateTable and SingleTable schemes, creates two indexes: second and third. First index ignored :(