public class MyPartRecordWithCollection : ContentPartVersionRecord
    {
        public MyPartRecordWithCollection()
        {
            this.Collection = new List<MyCollectionItem>();    
        }

        public virtual IList<MyCollectionItem> Collection { get; set; }
    }
 

public class MyCollectionItem 
    {
        public virtual int Id { get; set; }

        // some other properties

        public virtual MyPartRecordWithCollection MyPartRecordWithCollection { get; set; }
    }

this.SchemaBuilder.CreateTable("MyCollectionItem", table => table
                .Column<int>("Id", column => column.PrimaryKey().Identity())
                .Column<int>("MyPartRecordWithCollection_id"));

this.SchemaBuilder.CreateTable("MyPartRecordWithCollection", table => table.ContentPartVersionRecord());

Filters.Add(new MyStorageVersionFilter(repository))

public class MyStorageVersionFilter : StorageVersionFilter<MyPartRecordWithCollection>
    {
        public MyStorageVersionFilter(
            IRepository<MyPartRecordWithCollection> repository)
            : base(repository)
        {
            Logger = NullLogger.Instance;
        }

        public ILogger Logger { get; set; }

        protected override void Versioning(VersionContentContext context, ContentPart<MyPartRecordWithCollection> existing, ContentPart<MyPartRecordWithCollection> building)
        {
            // overriding the base copy logic to create new references rather than copying the existing ones
            CopyRecord(existing, building);

            // only the up-reference to the particular version differs at this point
            building.Record.ContentItemVersionRecord = context.BuildingItemVersionRecord;

            // push the new instance into the transaction and session
            _repository.Create(building.Record);
        }

        private void CopyRecord(ContentPart<MyPartRecordWithCollection> existing, ContentPart<MyPartRecordWithCollection> building)
        {
            Logger.Debug("Copy {0} {1}", existing, building);

            foreach (var existingCollectionItem in existing.Record.Collection)
            {
                var newCollectionItem = new MyCollectionItem();

                // Use existingCollectionItem to populate the new item - do it manually, use reflection, or however you prefer
                // I'm using ValueInjecter and I also set the Id to zero because it maps the old Id

                newCollectionItem.MyPartRecordWithCollection = building; // create relationship between the collection item and the new part record

                building.Record.ContentItemRecord = existing.Record.ContentItemRecord;
                building.Record.ContentItemVersionRecord = existing.Record.ContentItemVersionRecord;

                building.Record.Collection.Add(newCollectionItem);
            }
        }
    }

  public class MyHomepagePartRecord : ContentPartVersionRecord
  {
    public MyHomepagePartRecord()
    {
      Accommodations = new List<AccommodationTypeRecord>();
    }

    //public virtual string Teaser1 { get; set; }
    public virtual string RichTextBlock1 { get; set; }
    public virtual string RichTextBlock2 { get; set; }
    public virtual IList<AccommodationTypeRecord> Accommodations { get; set; }

  }

  public class AccommodationTypeRecord
  {
    public virtual string Name { get; set; }
    public virtual string Image { get; set; }
    public virtual string Url { get; set; }
    public virtual int Id { get; set; }
    public virtual MyHomepagePartRecord MyHomepagePartRecord { get; set; }
  }


 public class MyHomepageHandler : ContentHandler
  {

    public MyHomepageHandler(IRepository<MyHomepagePartRecord> repository)
    {
      //Filters.Add(StorageFilter.For(repository));
      Filters.Add(new MyStorageVersionFilter(repository));
    }

  }

  public class MyStorageVersionFilter : StorageVersionFilter<MyHomepagePartRecord>
  {
    public MyStorageVersionFilter(IRepository<MyHomepagePartRecord> repository)
      : base(repository)
    {
    }

    protected override void Versioning(VersionContentContext context, ContentPart<MyHomepagePartRecord> existing, ContentPart<MyHomepagePartRecord> building)
    {
      // overriding the base copy logic to create new references rather than copying the existing ones
      CopyRecord(existing, building);

      // only the up-reference to the particular version differs at this point
      building.Record.ContentItemVersionRecord = context.BuildingItemVersionRecord;

      // push the new instance into the transaction and session
      _repository.Create(building.Record);
    }

    private void CopyRecord(ContentPart<MyHomepagePartRecord> existing, ContentPart<MyHomepagePartRecord> building)
    {
      building.Record.ContentItemRecord = existing.Record.ContentItemRecord;
      building.Record.ContentItemVersionRecord = existing.Record.ContentItemVersionRecord;

      building.Record.RichTextBlock1 = existing.Record.RichTextBlock1;
      building.Record.RichTextBlock2 = existing.Record.RichTextBlock2;

      foreach (var existingCollectionItem in existing.Record.Accommodations)
      {
        var newCollectionItem = new AccommodationTypeRecord();

        // Use existingCollectionItem to populate the new item - do it manually, use reflection, or however you prefer
        // I'm using ValueInjecter and I also set the Id to zero because it maps the old Id
        newCollectionItem.Image = existingCollectionItem.Image;
        newCollectionItem.Name = existingCollectionItem.Name;
        newCollectionItem.Url = existingCollectionItem.Url;

        newCollectionItem.MyHomepagePartRecord = building.Record; // create relationship between the collection item and the new part record

        building.Record.Accommodations.Add(newCollectionItem);
      }
    }
  }