diff --git a/editor/editor_settings.cpp b/editor/editor_settings.cpp
index 7322e2aefb61..ec226bedecda 100644
--- a/editor/editor_settings.cpp
+++ b/editor/editor_settings.cpp
@@ -103,6 +103,14 @@ bool EditorSettings::_set_only(const StringName &p_name, const Variant &p_value)
 
 			builtin_action_overrides[action_name].clear();
 			for (int ev_idx = 0; ev_idx < events.size(); ev_idx++) {
+#ifndef DISABLE_DEPRECATED
+				// -3 was introduced in GH-97707 as a way to prevent a clash in device IDs, but as reported in GH-99243, this leads to problems.
+				// -3 was used during dev-releases, so this conversion helps to revert such affected editor shortcuts.
+				Ref<InputEvent> x = events[ev_idx];
+				if (x.is_valid() && x->get_device() == -3) {
+					x->set_device(-1);
+				}
+#endif // DISABLE_DEPRECATED
 				im->action_add_event(action_name, events[ev_idx]);
 				builtin_action_overrides[action_name].push_back(events[ev_idx]);
 			}