1. Create a host or a template.
2. Create LLD rule and an item prototype.
3. Create an application and assign it to the item prototype.
4. Export host/template.
5. Delete host/template.
6. Import with skipping the new application creation (unselect the checkbox "Applications - Create new").

3.0.0alpha3 successfully imports and simply skips importing the application for item prototype. It should've failed at least.

2.4. Fails to import, but the error message is incorrect:

Application with ID "" is not available on "host_test". [conf.import.php:190 ? CFrontendApiWrapper->import() ? CApiWrapper->__call() ? CFrontendApiWrapper->callMethod() ? CApiWrapper->callMethod() ? CFrontendApiWrapper->callClientMethod() ? CLocalApiClient->callMethod() ? call_user_func_array() ? CConfiguration->import() ? CConfigurationImport->import() ? CConfigurationImport->processDiscoveryRules() ? CItemPrototype->create() ? CItemPrototype->checkInput() ? CItemGeneral->checkInput() ? CApiService::exception() in C:\Development\zabbix-2.4\frontends\php\include\classes\api\services\CItemGeneral.php:398]

If item prototype has an application, it should fail to import in CConfigurationImport with an error that similar to normal items. For example "Item prototype "%1$s" on "%2$s": application "%3$s" does not exist.".