public partial class Entry
{
    public int Id {get; set;}
    public string Name {get; set;}
}

public partial class Entry2
{
    public Entry2()
    {
        this.Enrties = new HashSet<Entry>();
    }
    public virtual ICollection<Entry> Enrties {get; set;}
}

// list - содержит коллекцию элементов Entry2, внутри каждого из которых коллекция Entry
List<Entry2> list;

public partial class Entry : IEquatable<Entry>
{
    public bool Equals(Entry other)
    {
        if (Object.ReferenceEquals(other, null))
            return false;

        if (Object.ReferenceEquals(this, other))
            return true;

        return Id.Equals(other.Id) && Name.Equals(other.Name);
    }

    public override int GetHashCode()
    {
        int hashProductName = Name == null ? 0 : Name.GetHashCode();
        int hashProductCode = Id.GetHashCode();
        return hashProductName ^ hashProductCode;
    }
}

// для демонстрации заполним коллекции
List<Entry2> lst = new List<Entry2>()
{
    new Entry2()
    {
        Enrties =
            new List<Entry>()
            {
                new Entry() {Id = 1, Name = "1"},
                new Entry() {Id = 2, Name = "2"},
                new Entry() {Id = 3, Name = "3"}
            }
    },
    new Entry2()
    {
        Enrties =
            new List<Entry>()
            {
                new Entry() {Id = 3, Name = "3"},
                new Entry() {Id = 4, Name = "4"},
                new Entry() {Id = 5, Name = "5"}
            }
    },
    new Entry2()
    {
        Enrties =
            new List<Entry>()
            {
                new Entry() {Id = 5, Name = "5"},
                new Entry() {Id = 6, Name = "6"},
                new Entry() {Id = 7, Name = "7"}
            }
    },
};

var distinct = lst.SelectMany(x => x.Enrties).Distinct().ToList(); // 1,2,3,4,5,6,7