See the link here:
Basically, inside sources involved with production have said the show will have a time jump. However, the time jump is not to the Calypso future 1,000 years hence, but "only" 500 years in the future - in the 28th century.
Edit: I still don't understand how to square this with Georgiou staying on the show - unless she becomes main cast for the third season, and this is just a one-season diversion. Maybe Section 31 still exists in the 28th century, and for some reason they decide to hire her?