I had some similar issues. What worked for me, was to edit the web.config and save the file.

Hope it also works for you.

I also thought it would have something to do with caching, touching the web.config didn't help in my case. Nor did restarting the application.

I've also tried :

_contentService.RebuildXmlStructures();
_contentService.RePublishAll();

ExamineManager.Instance.IndexProviderCollection["MerchelloProductIndexer"].RebuildIndex();
ApplicationContext.Current.ApplicationCache.RuntimeCache.ClearAllCache();

But none of these are helping. There must be something else I'm missing.

What if you get all the products, and go through each of them and save them..

var productService = Merchello.Core.MerchelloContext.Current.Services.ProductService;
    var allProducts =productService.GetAll();

    allProducts.ForEach(x => productService.Save(x));

Haven't tested this, but something like that?

And run the index after that

Good suggestion. But unfortunately this does not work for me. Tried, saving all products, republishing all and rebuilding the product index. But still a 404 till I hit that save button in Umbraco.

I'll dive deeper into the Merchello source code to see what extra steps that save button does.

Finally got it working. Turned out the 'TemplateId' column in the 'merchProductVariantDetachedContent' table was empty. After filling that with the correct template id , everything works fine.

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