They can complete the flight, if the Captain feels it is safe to do so once they are airbourne. However, once the plane landed in San Juan, it would not have been legal to continue the journey to Rio. Sounds to me like the Captain got onto crewing, who advised a return to Charlotte because it was a whole lot easier to assemble a crew in Charlotte, their main hub, than try to get a crew out to San Juan and get the existing crew back.
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