First check in Shopify to see if you have 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, our integration won't be notified of the update made to the variant/product, and as a result, the update won't be reflected in Algolia.
You can try updating an additional product tag (for this purpose) at the same time as your metafield update, as the tag change would trigger a webhook to sync the data.