If you talk with a rationalist about making decisions via intuition, he has to grant you that their are domains of problems where intuition is very useful. Rationalism is about winning, so of course a good rationalist will use intuition for those domains.

If you look at medicine, In the last decade Cochrane has finally found that chiropractors can successfully treat back pain, even through their mental model of the human body conflicts with the model of mainstream medicine.

Most big mental systems get updated over time. As long as you do update towards new evidence, you don't have to trash your old beliefs completely.