Weren't 90s of deep breathing supposed to remove all cortisol in the blood? This seems like an opposite result. Also a single prolonged breath was supposed to reset autonomic nervous system. Which research should I trust now?

The title is inaccurate. The results are not about any kind of deep breathing or slow breathing.

The results are specifically about a breathing that is slower due to prolonged exhalation.

This kind of breathing is one of the many kinds of breathing traditionally practiced in yoga and also in many Asian martial arts, each kind for different purposes.

The experiments used in TFA have used a breathing rhythm of 2-second inhalation with 8-second exhalation, which is about the same as how I learned this kind of breathing as a child, from a yoga manual.

I have never heard about a single breathing of any kind to have much effect. For any kind of breathing rhythm you may need to use it from a large fraction of a minute up to a few minutes to have a noticeable effect.

As explained in TFA, this particular kind of breathing rhythm changes the balance between the 2 components of the autonomic nervous system, in favor of the parasympathetic nervous system.

This has the effect to diminish the influence that fear has on making decisions.

TFA is interesting because it provides a scientific confirmation about the usefulness of this kind of breathing rhythm, which has been traditionally used for centuries, if not even for millennia, in India, China and other Asian countries.