If you could answer whether I responded correctly to your what-if question.
Anyways, back to tips. I believe there should be a good method and reason to send the Abyss Watcher to Youkai Academy as a start of the story to build an intriguing premise.
For example, in Syn's case as a Hunter of the Workshop, there would have been two possible reasons for him to be sent to Youkai Academy, either by decapitation by Gehrman or being summoned by an unknown means (both of which being methods linked to the different endings of the game and still respecting the game's canon), with the second one being the method I took for my story. And so it ended up with Syn becoming a teacher for the very beasts he should be hunting, along with attempting to suppress his instincts to not begin a rampage as an interesting dichotomy.
But in the case of the Abyss Watcher, perhaps you could make the Abyss Watcher die to the Ashen One and have them reawaken at Youkai Academy after their death, with them having to deal with their comrades all dead. Or perhap you could make the Land of Farron itself teleport to Youkai Academy, bringing the Undead Legion along with it, since the lands converge together in Dark Souls all the time with disregard to time and space.