If the product is currently ticked in your Shopify integration's "Manage your Products" page, when it's obsoleted in Unleashed it will still remain synced with Shopify and will still export when "Export Products from Unleashed to Shopify" is actioned from the "Manage your Data" page. 

To stop obsoleted products from syncing or exporting to Shopify, make sure to untick the product in your Shopify integration's "Manage your Products" page before you make it obsolete in Unleashed. 

For more details, see Shopify: Manage your Products.