I may be mis-reading your note, but it sounds more like you have a list of IDs and want to know what user profiles are on the system that are not in the current employee ID file. If that is the case then there are various APIs and commands which can provide a list of user profiles. By checking this list against your employee file you could identify which profiles are no longer needed and perform the necessary cleanup. You will of course want to make sure you don’t inadvertently delete any profiles created by IBM products (or any other products you may have installed).
To get a list of profiles you could either use Security related commands/APIs or object related commands/APIs (asking for objects that are user profiles). For APIs, you might check List Authorized Users or List Objects.