Hah. Tru dat.So the moral of this story is, Check that all keys have good batteries in them and regularly check the keys work in all the locks. (Yes this has happened to me)
FWIW it wasn't the battery in the fob (it still reads 2.9v on the multimeter). I'm not sure quite what went on, because I took it to the local fob guy and the ECU happily re-paired to it.