A Rife machine will have no side effects, but may create a healing crisis, otherwise known as a Herx reaction, a detoxification response. Excessively large amounts of microbial or cancer cell waste and toxins hinder the body’s ability to adequately eliminate it through the usual channels (breakdown by the liver, through the colon or urinary tract).
So instead, the toxic material is discharged through the lungs, sinuses and skin. Symptoms can include a flu-like condition, heavy perspiration and night sweats, fever, with or without chills, headaches, malaise, diarrhea, nausea and vomiting, pain in joints and bones, and itching, flushing, and reddening of skin.
The above can apply to even a detox protocol where toxins are not being produced by die off, but are being released back into the bloodstream from where they were hiding (joints, muscle tissue, etc.).
If this happens your likely target is eliciting a response. Could be an indication that there is a lot of work to be done by these frequencies and may have done too much too fast.
Try a lower amplitude setting next time you run these sets. Suggest you take a break until your body is able to flush out what toxins it is processing.