There are several services in the portal where the Autogenerated methods of the *ServiceBaseImpl.java have a very similar name to the manually implemented services in *ServiceImpl.java but the functionality is completely different.
This happens in almost every service in Portal. For example, in Document Library we have the following API:
This following method checks if there are related DDMStructures and is deleting those too and then deletes FileEntryType.
However, this other method DLFileEntryTypeLocalServiceBaseImpl.deleteDLFileEntryType(..) which calls DLFileEntryTypePersistence layer to delete FileEntryType. This might lead data corruption!
Then, the developers may be confused because they don't know which API should be called deleteFileEntryType or deleteDLFileEntryType.