To be clear... Hibernate scans and keeps track of the names of entity, embeddable and mappedsuperclass classes it found: just the name effectively. Later it will convert them into Class references using the ClassLoaderService. So something in that process would have to go awry.

Maybe some static reference in that process.

Maybe ClassLoaderService sees too much? But even then, for it to be inconsistent would mean some inconsistency in how the ClassLoaderService's aggregated ClassLoaders are built.