::::Are you sure that the name "Voskopojë" wasn't used in the 18th century, by Albanian speaking locals? I'm not surprised the Greek name Moschopolis shows up more frequently in older literature, Greek was the language of the church and education in the southern Balkans then (also in Ohrid, for instance). Anyway, what's more relevant is under what name the place is referred to in contemporary English. Google Scholar is undecided (also if you count all M-versions together, it's 24 vs. 21). There are far more hits in Google Books (652 since 1959), I checked the hits of the past 5 years Google Books, these are the results: 
 ::::*Moscopole 1 
 ::::*Moschopolis 14 
 ::::*Moschopole 1 
 ::::*Voskopojë/a 14 
 ::::*Moscopolis 0 
 ::::*duplicate 10 
 ::::*not about town 10 
 ::::*not in English 15  
 ::::My confirmed conclusion: English usage is evenly divided between Moschopolis and Voskopojë/a.