The part I think you are missing is using the Personal Status Code on each person's profile. The personal status code is used to indicate that individual's relationship with the church. So if someone is a member, you mark them as a member, if they are visitor, you marked them as a visitor. When someone passes away you can change their status to deceased, if they move away you can mark them as a former member, etc.
When you run the church directory you can then say you want to only include people with the specific status codes. For instance members, children of members, regular attenders, etc. And only those people with those status codes will show up on the directory.
Deceased directory number
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