You can't beat Watcher's Keep twice.
If you have completed it already in SoA, then it will be completed in ToB. The status of Watcher's Keep is kept when you transit from SoA to ToB.
Anyway...
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... you can re-visit Watcher's Keep after you find a way out of Saradush, which is a city you enter after you find a way to exit the Pocket Plane.