We have deployed app to prod environment back in 2020. After a few years it turned out that some features are not needed. We have deleted those objects on our dev environment then on git repo. During deployment to UAT or PROD based on version control system package.zip is created. This package does not contains deleted objects. This package is pushed to higher environment by Appian API - during deployment objects not available in package are not deleted from higher environment but Appian just remove them from deployed application. In other words objects remain in higher environment as not linked to particular application.
How to use automated deployment via API and delete objects from higher environment automatically ?
docs.appian.com/.../Deployment_Rest_API.html
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You can remove the objects during the deployment which you did not want to deploy but deleting is not possible or also not recommended by appian you can make unused object application in your env and can add those object which ae of no use for your application. In that way it will be seperated.