Canon is rather inconsistent, as you’d expect. In MoR chapter 23 there’s this:

He'd put everything he had into the Finite Incantatem and it still wasn't working. Some hexes required specific counters or you couldn't undo them, or maybe it was just that Draco was that much stronger.

Stuff like locks would obviously be protected, but Harry’s thoughts (“some”) suggests that it’s more of an exception.