Dear Kiki,
Without evaluating him, I cannot say for sure what is happening. It could be gastroesophageal reflux causing the heart rate to fall and then come back up. It also could be secondary to the cerebral palsy, as we do see patients who have abnormal control of their autonomic nervous system (the part of the nervous system that automatically controls heart rate, blood pressure, etc.) in those children who have brain abnormalities. However it is more important to note whether this is affecting him adversely or not. If he is tolerating it well, behaving normally, and not having any problems, a heart rate in the 40's in an 11 year-old typically shouldn't cause any major concerns. If it is causing increased seizure activity or other issues, it may need to be treated.
Thank you so much ,that was very helpful to knowing what could cause his heart rate to drop ,so I will continue to monitor him and if I see any changes I will contact his primary care physician.