Ohh... I forgot =D Any changes that I make to the object graph after DeSerializing to Json needs to be serialized back again =D

Here is a working example:

public class RichTextEditorCleanupOnSaveHandler : 
INotificationHandler<ContentSavingNotification>
{
public void Handle(ContentSavingNotification notification)
{

    foreach (var entity in notification.SavedEntities)
    {

        foreach (var property in entity.Properties)
        {
            if (property.PropertyType.PropertyEditorAlias == "Umbraco.BlockList")
            {

                string rawJson = property.GetValue().ToString();

                BlockValue blockValue = JsonConvert.DeserializeObject<BlockValue>(rawJson);

                foreach (var column in blockValue.ContentData)
                {
                    foreach (var columnProperty in column.RawPropertyValues)
                    {
                        // this contains other blocks
                        var block = JsonConvert.DeserializeObject<BlockValue>(columnProperty.Value.ToString());

                        if(block == null)
                            continue;

                        foreach (var blockData in block.ContentData)
                        {
                            foreach (var blockProperty in blockData.RawPropertyValues)
                            {
                                if (blockProperty.Key == "body")
                                {

                                    blockData.RawPropertyValues["body"] = new HtmlInputCleaner().CleanUp(blockProperty.Value.ToString());
                                }
                            }
                        }

                        column.RawPropertyValues[columnProperty.Key] = JsonConvert.SerializeObject(block);

                    }
                }

                property.SetValue(JsonConvert.SerializeObject(blockValue));

            }
        }

    }
}
}