I like how your thinking coming up with new ideas but since the copper does clear the parasite for 1-2 month would this not rule this out? I have not read the article..
There actually is no evidence of "copper resistant" protozoans, just anecdotes. Most cases stem from improper treatment. In this case, using copper power at too low of a dose for only half the normal treatment time. True genetic resistance is pretty rare - it takes generations of the parasite being exposed to sub-lethal doses of a medication.
Jay