this_works.ex

spec = %{
  commands: [
    %{name: "abc", ...},
    %{name: "def", ...},
    ...
  ]
}

...

# we have {key, val} defined
index = Enum.find_index(spec.commands, &(&1.name == key))
if !index, do: config_error("Unrecognized command: #{key}")

cmdspec = Enum.at(spec.commands, index)
Map.update!(spec, :commands, fn list ->
  List.replace_at(list, index, Map.put(cmdspec, :action, val))
end)

wish_this_worked.ex

index = Enum.find_index(spec.commands, &(&1.name == key))
if !index, do: config_error("Unrecognized command: #{key}")

put_in(spec.commands<[index]>[:action], val)