We use relative hyperbolicity of mapping tori and Dehn fillings of relatively hyperbolic groups to solve the conjugacy problem between certain outer automorphisms. We reduce this problem to algorithmic problems entirely expressed in terms of the parabolic subgroups of the mapping tori. As an immediate application, we solve the conjugacy problem for outer automorphisms of free groups, whose polynomial part is piecewise inner. This proposes a path toward a full solution to the conjugacy problem for $\mathrm{Out}(F_n)$.