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As of right now, Southwest Airlines flies to three different cities within Cuba – Havana, Varadero, and Santa Clara. But to probably no surprise, they will be consolidating those flights on Monday September 4, 2017 and will only service Havana airport (service to Varadero and Santa Clara is being cancelled). Like many airlines, Southwest over anticipated the amount of passengers that would be flying to Cuba.
If you have a Southwest flight to either Varadero or Santa Clara on September 5, 2017 or beyond, Southwest Customer Service should be getting in touch with you. If you are impacted, I personally would ask for some sort of good will gesture as this might heavily impact your travel plans. Southwest is typically pretty good with customer service gestures, so hopefully they make it right.