Having gone through old stats, I realise that I have seen this happen before (total collapse in CTR and earnings) back in 2010.
I fixed it back then by changing the ads from my company's adsense account to my personal account. Suddenly the CTR and earnings improved. Unfortunately I don't have that option any more (to change adsense accounts).
Another observation is that I get credited with some clicks at a certain rate, only for that rate to be reduced massively a few minutes later. Irrelevant ads being smart-priced down?