If the treatment is indeed killing pathogens, this will induce stress to the body and as a result the heart rate can definitely increase. This is the very principle that biofeedback uses to identify frequencies that the body indicates are useful for addressing issues.
As for the ultrasonic cover, this is to decouple any possible chance of electrical flow from the ultrasonic wand to your body, or from the body back to the SC. So it is best to leave it on.
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