The mutual consistency of boundary conditions twisted by an automorphism group G of the chiral algebra is studied for general modular invariants of rational conformal field theories. We show that a consistent set of twisted boundary states associated with any modular invariant realizes a non-negative integer matrix representation (NIM-rep) of the generalized fusion algebra, an extension of the fusion algebra by representations of the twisted chiral algebra associated with the automorphism group G. We check this result for several concrete cases. In particular, we find that two NIM-reps of the fusion algebra for $su(3)_k (k=3,5)$ are organized into a NIM-rep of the generalized fusion algebra for the charge-conjugation automorphism of $su(3)_k$. We point out that the generalized fusion algebra is non-commutative if G is non-abelian and provide some examples for $G = S_3$. Finally, we give an argument that the graph fusion algebra associated with simple current extensions coincides with the generalized fusion algebra for the extended chiral algebra, and thereby explain that the graph fusion algebra contains the fusion algebra of the extended theory as a subalgebra.
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