Application prototypes support LLD macros.
One application prototype can be used by several item prototypes of the same discovery rule.
If created application prototype is not used by any item prototype it gets removed from 'Application prototypes' list automatically.
Like other discovered entities applications follow the lifetime defined in discovery rule ('keep lost resources period' setting) - they are removed after not being discovered for the specified number of days.
If an application is not discovered anymore, the application itself may not be removed because of the 'lost resources period' setting, however:
Application prototypes defined by one discovery rule can't discover the same application. In this situation only the first prototype discovery will succeed, the rest will report appropriate LLD error. Only application prototypes defined in different discovery rules can result in discovering the same application.