No, you have to re-upload the _lib any time NetMake updates ScriptCase and you have to re-deploy an updated app of your own.
NetMake has broken my deployments with _lib changes several times over the years. I call this a “ScriptCase IPM” event: Instant Panic Mode.
The alternative is to use Git to save your entire ScriptCase deployment environment so that, if you have to update one of your apps, you can restore the ScriptCase environment to the original deployment state, verify that your app still works with that version of ScriptCase, deploy the app, then restore the latest version of ScriptCase.
I kind of get the impression that NetMake doesn’t use ScriptCase. or, at least, that they have never thought-through a ScriptCase user’s workflow or their project’s lifecycle.