Have you ever heard the term crisis healing? It's where the healing process gets so intense that it feels bad when the outcome is actually good (blessing in disguise kind of thing).
In the Craft, we use salt water to collect up energies from Earth and Water to cleanse them. We use insence to collect and cleanse Fire and Air energies. Using negative energies within your chakras might actually collect up the rest of the negative energy and cleanse it as well (like a purging) - this is a fine example of a crisis healing.