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So I've read the online PDF rules and can't seem to find an answer for this.
After scoring points in a round with the wagon, if you move the wagon to another unfinished city or road as per the wagon rules, does this count towards deploying a new follower and stop you from taking control of the fairy from the "Princess And The Dragon" expansion?
No. Redeployment of the Wagon following scoring (at the end of a turn) is a separate step from the figure deployment step (for the next turn), so it has no effect on any of the actions you can take during the figure deployment step, including moving the Fairy.