Watcher's Keep will be in TOB exactly in the same state you left it in SoA. F.e., if you have completed only two levels of it in SoA, then in ToB you find that two levels are completed...
So, you'll be able to finish all you business in the Keep right from the point you've left it in SoA.
Good luck
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Tanda,
with best regards from Guild of Assassins