But the end result is just a warning message right? Nothing is actually fatally broken?
Not on my system, at least.
Apparently, I've been living with that message for a long time without ever noticing it. 
Apparently, I've been living with that message for a long time without ever noticing it.
Same. It's just that the devs decided for whatever reason to treat this as a fatal error which obviously got me concerned. I think I'll just remove the ~/.gnupg folders then and ignore the error for the time being.