Forum Discussion
You played rotationally with aging on so he died of old age. When a Sim you are not currently playing dies no Urn or Grave is created.
@simplyshiny514 In addition to that; and for the genealogy/family tree:
Bug report for butchered family tree:
https://answers.ea.com/t5/Bug-Reports/NEEDS-INPUT-Sims-in-Family-Tree-Disappearing/td-p/7287642
Bug report for missing ghosts in family tree after using CAS:
https://answers.ea.com/t5/Bug-Reports/NEEDS-INPUT-Sims-disappearing-from-family-tree-after-entering/td-p/7827487
If they fit your issue, please provide any saves you have from before the culling. Also clicking Me Too on the first post will give the bug report some more weight.
Descriptions on how to provide a save:
https://answers.ea.com/t5/Bug-Reports/INFORMATION-How-to-Send-User-Files-to-The-Sims-4-Team/td-p/6065302