Today, if you have a workspace template that’s part of a live app, changing the boards in the workspace while the app is a Live version results in changes to the workspace when deployed by end users. This seems counter to having app versions, as it makes it entirely possible to corrupt a template inadvertently after going live (and means development requires duplicating the workspace for the next version to do any work on it.)
When an app version changes to live, it should snapshot the workspace someplace outside the dev account, and end-user deployments should be based off the snapshot - not off the workspace the template is based on.