No worries. Filters often have black carbon additives to remove odors and smells...they also remove medication (and trace elements, hence my dislike of them)...when you medicate, you do not want carbon filtering or medication is useless.
Also, when medicating, a temporary bump in temp can be very helpful. Some fish I used to keep did best with certain illness when water temp was increased above 90 degrees.
A 100% wc is bad. It will over stress the fish and potentially kill the biological filter. Ideally, fish never come out of their tanks during cleaning, ever, and 50% WC with gravel vaccing are the max. The instructions probably says 25-50% after every 24-48 hours with redosing after for something like 7-14 days. At no point is there a need to do a full and complete cleaning given it will wipe out nitrifying bacteria and lead to the tank needing to re-cycle, potentially harming fish heath. After treatment, carbon can be re-added to remove any medication a 50% WC does not, or even better a filter media like Purigen.
Other components will not be affected. It will kill what it in the eggs, but only when they hatch as it kills mainly in the free swimming stage. Increased temps speed the lifecycle of parasites and also speed the metabolic rate of fish.
Even more so than normal, testing water frequently is a must too. Bad water parameters are a roadblock to healing.