Yep, archiving feature flags and deleting the dead code is usually thing number 9001 on the list of priorities, so in practice most projects end up with a graveyard of them.

Another issue that I've ran into a few times, is if a feature flag starts as a simple thing, but as new features get added, it evolves into a complex bifurcation of logic and many code paths become dependent on it, which can add crippling complexity to what you're developing