For anyone who had the similiar issues, I finally got solution (Note: you need to upgrade to EPi.Find.Commerce 9.5.2+).  

        protected override void IndexContentsIfNeeded(IEnumerable<ContentReference> contentLinks, 
            IDictionary<Type, bool> cachedReindexContentOnEventForType, 
            Func<bool> isReindexingContentOnUpdates)
        {
            var contents = _contentRepository.GetItems(contentLinks, CultureInfo.InvariantCulture).ToList();
            var parentContentLinks = new List<ContentReference>();
            foreach (var parents in contents.OfType<VariationContent>().Select(content => _contentRepository
                .GetItems(content.GetParentProducts(_relationRepository), CultureInfo.InvariantCulture).Select(c => c.ContentLink).ToList()))
            {
                parentContentLinks.AddRange(parents);
            }
            IndexContentsIfNeeded(parentContentLinks, GetIndexContentAction());
        }