Quick update, this was finally sorted yesterday morning after two further phone calls and three e-mail messages to the EC. The final phone call ended with a very competent-sounding agent promising to make a manual adjustment to the TPs but actually just ended up re-crediting the flights at the wrong rate. So a couple of e-mail messages later I get a response from the EC stating that partner flights booked before the 28th April should be credited at the new earnings rate, but as a "gesture of goodwill" because I'd been "misadvised" of this, they had made a manual adjustment and I got the 140 TPs. So, perseverance wins out.