Dear Librarian,
I understand that early in givewell history the team considered poverty or health in rich countries and found these areas to be less cost effective than in poor countries. I imagine that many organizations go through a similar process. It would be interesting and useful to review these causes and evidence for rejection from many organizations.
Warmest regards
I agree that collections of "we investigated a possible intervention/focus area and decided not to go for it for XYZ reasons" could be a really useful resource.
It's also probably worth emphasizing that there aren't causes that are universally rejected by EA as a community or movement. (As you say, this might be organization-specific: some organizations will have decided to focus on some "causes" -- specific risks, or specific philosophies or approaches to improving the world -- over others.)
I don't have a good answer to this, but I will say that the following two tags could have useful or relevant materials for approaching these questions:
(Not answering on behalf of the librarian program.)