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We define the orbit morphism of partial dynamical systems and prove that an orbit morphism being an isomorphism in the category of partial dynamical systems and orbit morphisms is equivalent to the existence of a continuous orbit equivalence between the given partial dynamical systems that preserves the essential stabilisers. We show that this is equivalent to the existence of a diagonal-preserving isomorphism between the corresponding crossed products when the essential stabilisers of partial actions are torsion-free and abelian. We also characterize when an \'etale groupoid is isomorphic to the transformation groupoid of some partial action. Additionally, we explore the implications in the context of semi-saturated orthogonal partial dynamical systems over free groups, establishing connections with Deaconu-Renault systems and the concept of eventual conjugacy. Finally, we apply our results to C*-algebras associated with generalized Boolean dynamical systems., Comment: 24 pages

We prove the Effros-Hahn conjecture for groupoid algebras with coefficients in a sheaf, obtaining as a consequence a description of the ideals in skew inverse semigroup rings. We also use the description of the ideals to characterize when the groupoid algebras with coefficients in a sheaf are von Neumann regular, primitive, semiprimitive, or simple. We apply our results to the topological dynamics of actions of inverse semigroups, describing the existence of dense orbits and minimality in terms of primitivity and simplicity, respectively, of the associated algebra. Moreover, we apply our results to the usual complex groupoid algebra of continuous functions with compact support, used to build the C*-algebra associated with a groupoid, and describe criteria for its simplicity.