Using the Batalin-Vilkovisky formalism, we study the Ward identities and the equations of gauge dependence in potentially anomalous general gauge theories, renormalizable or not. A crucial new term, absent in manifestly nonanomalous theories, is responsible for interesting effects. We prove that gauge invariance always implies gauge independence, which in turn ensures perturbative unitarity. Precisely, we consider potentially anomalous theories that are actually free of gauge anomalies thanks to the Adler-Bardeen theorem. We show that when we make a canonical transformation on the tree-level action, it is always possible to re-renormalize the divergences and re-fine-tune the finite local counterterms, so that the renormalized $\Gamma $ functional of the transformed theory is also free of gauge anomalies, and is related to the renormalized $\Gamma $ functional of the starting theory by a canonical transformation. An unexpected consequence of our results is that the beta functions of the couplings may depend on the gauge-fixing parameters, although the physical quantities remain gauge independent. We discuss nontrivial checks of high-order calculations based on gauge independence and determine how powerful they are.