First of all, check in Shopify to see if you have you added the metafields on variants or on products.
Variant metafield updates don't trigger the products/update webhook on the Shopify side. If we (Algolia) do not receive a webhook request from Shopify, we won't know that an update has been made to the variant/product.
You can try updating an additional product tag (something just for this purpose) at the same time as your metafield update, as the tag change would trigger a webhook to sync the data.