Based on your explenation, this can only happen if the products disappear, then re-appear. Manually edited product details can not vanish by itself. The only case it can happen, is when the product has disappeared. Either this is an app issue or something with Shopify.
Yes, it possible removing account details will delete all products.
My recommendation is to either contact Google for this issue: https://support.google.com/merchants/contact/shopify_3p_support_app
Or use a much better app such as: https://apps.shopify.com/multiple-google-shopping-feeds