Why are your retired integration workflows being republished after restarting your server?
This is working as designed. The integration object is controlled by the platform, so any changes it finds will be added back upon an application server restart. You can find more information in the IBM Knowledge Center topic: Object upgrades. Note that if you add an integration object record called IGNORE_UPGRADE, then no updates will be made to the integration object and it will not apply fixes in the future that are added to the package.