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Remember that there are two kinds of miles:
- "Banked miles" are a currency you earn based on flying, using credit cards, renting cars, staying in hotels, etc. Banked miles accumulate in your account indefinitely until you "spend" them on award flights.
- "Elite qualifying miles" (EQMs) are a system that keeps track of your flying each year to determine your elite status. You start with 0 EQMs on January 1, and earn EQMs based solely on how many miles you fly in which fare classes during the course of the calendar year. You cannot earn EQMs from credit card usage or other non-airline partners (except Amtrak), and you cannot "spend" EQMs.
For a given flight, you earn both banked miles and EQMs. For example, a single flight EWR-CDG will earn about 3,650 banked miles and 3,650 EQMs if booked in coach and purchased through continental.com (as you've learned, you earn only 50% EQMs on cheap fares purchased elsewhere, and you can earn 150% EQMs for expensive fares and business class). You may also earn bonus banked miles for certain promos, or if you're elite (CO silver elites earn a 50% banked mile bonus on all CO and most partner flights).
One other thing to note: Several CO partners (AF, AZ, DL, KL, NW, etc.) also fly to CDG, and you can boost your mileage earning by taking routings that are less direct. For example, EWR-CDG is only 3,650 miles nonstop, but NYC-DTW-AMS-CDG on NW/KL earns over 4,900 miles (and will earn 100% EQMs if booked in NW "Q" class, which is often similarly priced to CO's transatlantics). Flying AZ NYC-FCO-CDG earns almost 5,000 miles each way, and you may be able to find competitive 100% EQM fares from AZ, too.