The main engines are the nine engines that is attached to the first stage that they land. The secondary engine is on the upper stage which they do not recover. So the main engines are recovered from the landed first stage and then refurbished to be reused. Your confusion might come from other rocket designs such as the Space Shuttle or the Delta V which use booster rockets. The main engines still light up at liftoff but do not provide most of the thrust until the boosters are out of fuel. So with these rockets the main engine stay attached until they reach orbit, or at least almost to orbit. But this is not how the SpaceX rockets are configured.
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