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Just a reminder from the guidance on Biographies
All profiles should have these sections:
== Biography == == Sources == <references />
The sources section should always have a <references /> tag even if there aren't any footnoted references yet.
So that extra work to remove the Biography heading or the references tag is not needed
Matthew, there is a known situation where use of the WikiTree X extension can remove the required lines. However, this is because WikiTree X is no longer being maintained. See this post from Jamie Nelson, who recommends that WikiTree Sourcer be used instead.
If you are seeing a method of profile creation not involving WikiTree X where the headers or references line end up missing, that may be a new, not yet known error. Are you able to give more detail?