My daughter has cchs- her dr seems puzzled when we explain that her o2 sats run low, while still maintaining an appropriate co2 level. The best they have come up with is malacia- she shows no signs of pulmonary hypertension. What else should we have rul

A few things. As you know, cchs is a rare condition and is not fully understood. There are a number of diseases that are associated with and syndromic with cchs. An example is hirschprungs disease, which seems to share a link with an underlying genetic defect that also can cause cchs. The best way to evaluate is a pulmonoligist affiliated with a children's hospital that has a wide range of subspecialities.
CCHS. I presume you are referring to congenital central hypoventilation syndrome. Cchs is a multisystem disorder of the central nervous system where, most dramatically, the automatic control of breathing is absent or impaired. A cchs patient’s respiratory response to low blood oxygen saturation (hypoxia) or to co2 retention (hypercapnia) is abnormal. I suggest you seek out a specialist in cchs.