Once you have 50 ancestors, it'll start automatically deleting the oldest ones chronologically.
There's a file in your ANCESTORS directory called lastentry.txt that is just the number of the last character that died. When a character of mine dies, I edit it to be the number before my shortest lived ancestor so that this one gets overwritten instead, because I want my ancestors to be the characters that lived a long time and I put a lot of energy into them, not the characters that died on day 1 because i couldn't escape the njerpez camp.