If you converted from Recharge Checkout on Shopify to Shopify Checkout Integration, auto-renew products should not be deleted unless you are confident your store does not rely on auto-renew to provide existing customers with subscription-specific shipping rates. Deleting them will disrupt the subscription-specific shipping rate provided to existing customers, and they can not be recreated once deleted.

Hidden auto-renew products were created when creating a subscription rule in the previous legacy platform, Recharge Checkout on Shopify. Recharge used the auto-renew product to verify the subscription price and product title that you set up during checkout, while the original product in your store was used for all other related information, such as inventory. 

The auto-renew product was only used when a customer checks out with a subscription product. Recharge could get the relevant product information without the auto-renew product if a subscription was created through the merchant portal, the customer portal, or through the API.