Two years ago we booked Jet Blue for FLL to SXM via SJU. About two months prior to departure they cancelled the return due to a schedule change.
I called JB and they explained that before the schedule change we had 1:31 to clear customs and get to our gate but that after the schedule change we had 1:28 to get there. The computer wouldn't allow a connection unless there was 45 minutes to change for a domestic flight and 1:30 if you had to clear customs and immigration. A supervisor over rode the system and we had plenty of time to make the connection.
I suppose that it's possible to book the legs independently if that makes logical and financial sense to you.
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