Have them emit metrics when it's triggered. You can do a bulk "names X, Y, Z haven't used branch B in >30 days, delete?" task generator pretty easily. Un-triggered ones are also easy to catch if you force all calls to be grep-friendly (or similar), which is also an easy lint to write: unclear result? Block it, force `flag("inline constant", ...)`.

Personally I've also had a lot of success requiring "expiration" dates for all flags, and when passed they emit a highly visible warning metric. You can always just bump it another month to defer it, but people eventually get sick of doing that and clean it up so it'll go away for good. Make it mildly annoying, so the cleanup is an improvement, and it happens pretty automatically.

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