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We study the deformation theory of fully faithful Fourier-Mukai transforms in both characteristic zero and mixed characteristic. Our main result shows that obstructions to deforming such transforms can be completely controlled by Hodge theory when the source variety has trivial canonical bundle, generalizing work of Addington-Thomas and Lieblich-Olsson. The main technical contribution is a formula for the obstruction class measuring the failure of a Chern character to remain within the Hodge filtration as a cup product with a (derived) Kodaira-Spencer class.

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