My understanding is that these beans are simple java objects, but once they have survived being removed at build-time and have been (lazily) initialized, they are held in the context indefinitely and should not be GC-able even if they are idle for long times.
But I was unable to confirm it after running through the 2.0 CDI specs and the bean lifecycle/CDI related Quarkus docs.
Are there any specific cases where this could happen?
So in theory, you can do AlterableContext#destroy(Contextual<?>) - this would remove the contextual instance (i.e. the instance of your @ApplicationScoped bean) from the context, and then it can be garbage-collected if there are no other references.
For example, in quarkus you can do Arc.container().instance(MyApplicationScopedFoo.class).destroy(). This would call the @PreDestroy callback if present, @PreDestroy interceptors if bound, and remove the MyApplicationScopedFoo instance from the application context.