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Don't do any treatments in your main tank. Copper and hyposalinity will kill your inverts. Copper will also bind with the silicone, sand, and live rocks in your tank meaning that any equipment used can only be used with a FOWLR system from that point on. Get you a cheap 20L and some PVC and do a hospital tank. If you have more fish you may want to get a bigger tank.
And just so you know you`ll see the parasites on your fish and the next thing you know they are gone. Most people think they just disapeared when in reality they dropped off the fish and over 200 little ones called tomites will come from each one that dropped off. So to answer your question no they are not gone but will return with a vengence. Need to QT your fish and treat. Your main will need to be fishless for 8 weeks to break the parasite.